feat(doctor): scripts/doctor.py owns core; retire legacy framework_doctor + hook (#1335 #1336)#1380
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MScottAdams merged 4 commits intoMay 30, 2026
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@greptileai review Standard PR from swarm 1334 (stories #1335 #1336). Full review cycle in progress per approved workflow. Monitor will handle fixes iteratively until CLEAN. |
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⚠️ Superseded by a newer SLizard review
⚠️ Superseded by a newer SLizard review
⚠️ Superseded by a newer SLizard review
Machine-readable verdict
{
"slizard_verdict": {
"schema_version": 1,
"decision": "comment",
"severity": {
"P0": 0,
"P1": 0,
"P2": 0,
"P3": 0
},
"confidence": 0.3897,
"decision_confidence": 0.3897,
"finding_count": 0,
"merge_impact": "non-blocking",
"version": "slizard v0.3.951",
"head_sha": "84592659705a7bebbc31c6ec61ee7995b19e576a"
}
}⚙️ Refactor PR — file reorganization detected (1 file(s) reorganized, 791 lines moved).
P2 · scripts/doctor.py:124 · confidence 0.70
except Exception catches nearly all exceptions. The handler body does not re-raise, so errors are silently swallowed. Catch a narrower type or re-raise the exception.
P2 · scripts/doctor.py:108 · confidence 0.70
Path.cwd() used outside a CLI entry point to construct a file path. When the working directory differs from the project root (e.g. Taskfile dispatch, test runners, CI), the resolved path silently points elsewhere. Use a config-rooted path, __file__-relative resolution, or an explicit parameter instead.
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%% 611 additional affected node(s) omitted for diagram size
Review coverage
- Reviewed files:
CHANGELOG.md,run,scripts/doctor.py,scripts/framework_doctor.py,tests/cli/test_framework_doctor.py,tests/cli/test_framework_doctor_prose.py,tests/cli/test_install_manifest_root.py - Skipped files: none
- Source: github @
84592659705a
Context used
- Static findings: 10
- Static tools: dangling-reference; mixed-dict-access-pattern; python-exception; python-path-construction; unused-export
- Graph/blast radius: 68 changed node(s), 611 affected node(s)
- Vector context chunks: 12
- Context availability: full
- Review categories: default
- Deterministic checks:
349/358 passed, 9 failed: unused-exports, python-exception, python-path-construction, dangling-reference, mixed-dict-access-pattern, graph-incompleteness, graph-callsite-not-updated, orphaned-module, graph-validation-gap
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go-json-field-exposure=passed, go-mutable-exported-slice=passed, go-silent-error-branch=passed, go-comment-log-contradiction=passed, go-unconditional-message=passed, inline-style-proliferation=passed, unnecessary-nonnull-assertion=passed, double-cast=passed, unguarded-await-cast=passed, ssrf-guard-completeness=passed, error-message-leak=passed, puppeteer-resource-cap=passed, trivial-argument=passed, unused-imports=passed, dead-store=passed, phantom-import=passed, fetch-timeout-guard=passed, log-level-expected-path=passed, unified-diff-construction=passed, sentinel-index-assertion=passed, unguarded-map-lookup=passed, unbounded-prompt-injection=passed, description-diff-consistency=passed, render-branch-symmetry=passed, go-gorm-unchained-error=passed, go-gorm-rowsaffected-noop=passed, error-handling-loop-break=passed, sync-state-batching=passed, sync-revoke-object-url=passed, go-like-wildcard-injection=passed, go-basename-dedup-gap=passed, go-missing-seed-in-migrate=passed, go-write-then-read-unfiltered=passed, go-direct-db-access=passed, async-handler-try-catch=passed, chat-sdk-history=passed, dead-code-ternary=passed, go-context-background=passed, go-git-arg-order=passed, go-n-plus-one=passed, go-nested-transaction=passed, go-ref-injection=passed, go-scanner-error=passed, go-toctou-db=passed, go-unused-validated-field=passed, hardcoded-literal=passed, hardcoded-undefined-field=passed, python-exception=failed, python-path-construction=failed, python-isdigit-int=passed, deprecated-python-utcnow=passed, python-variable-shadow=passed, frozen-dataclass-mutable-field=passed, sentinel-value=passed, sibling-constant=passed, url-interpolation=passed, jsx-guard-removal=passed, asymmetric-clamp=passed, optional-prop-guard=passed, server-lifecycle=passed, go-asymmetric-org-scope=passed, fetch-body-scope-omission=passed, regex-breadth-inconsistency=passed, typeof-object-array-guard=passed, test-production-divergence=passed, argument-axis-mismatch=passed, click-propagation-gap=passed, sanitization-gap=passed, response-shape-consistency=passed, keydown-target-guard=passed, changelog-test-count=passed, unbounded-metadata-assignment=passed, unchecked-json-response=passed, response-body-leak=passed, json-syntax=passed, requestid-route-param=passed, dict-key-as-value=passed, redundant-transitive-call=passed, incomplete-iteration=passed, call-site-parameter-consistency=passed, markdown-heading-level=passed, cross-section-order-contradiction=passed, dangling-reference=failed, useref-dead-store=passed, fetch-redirect-guard=passed, response-body-buffering=passed, svg-content-type=passed, conditional-mode-exclusion=passed, join-separator-inconsistency=passed, prompt-injection-guard=passed, asymmetric-guard=passed, unsafe-json-cast=passed, storage-unsafe-cast=passed, markdown-single-line-interpolation=passed, postmessage-origin-guard=passed, css-iframe-scope=passed, markdown-entry-completeness=passed, python-set-duplicate=passed, state-setter-symmetry=passed, changelog-sibling-truncation=passed, ternary-exhaustiveness=passed, exclusive-output-constraint=passed, nullish-fallback-regression=passed, shell-pipefail=passed, vbrief-acceptance-contradiction=passed, css-property-diff=passed, go-sync-call-labeled-background=passed, prompt-guardrail-conflict=passed, prompt-identity-duplication=passed, asymmetric-truncation=passed, claim-source-tracing=passed, go-duplicate-event-publish=passed, go-create-without-cleanup=passed, go-find-then-create-without-cleanup=passed, go-persist-without-validate=passed, ts-put-without-get=passed, go-fetch-id-without-liveness=passed, go-event-subscribe-without-publish=passed, go-log-aggregation-run-scoping=passed, falsy-string-fallback=passed, useeffect-unstable-prop-dep=passed, unused-state-read=passed, blob-mime-mismatch=passed, parseint-nan-guard=passed, shared-state-across-map=passed, context-menu-click-guard=passed, touch-action-ancestor=passed, usestate-innerwidth-matchmedia=passed, prefix-match-loop=passed, hardcoded-new-field=passed, enum-subset-completeness=passed, optional-guard-fallthrough=passed, html-template-token=passed, label-association=passed, empty-src-img=passed, jsx-prose-link-mismatch=passed, try-catch-scope=passed, viewport-meta-accessibility=passed, go-github-api-response-id=passed, go-github-api-pagination=passed, go-gorm-first-without-errrecordnotfound=passed, fetch-cache-consistency=passed, oauth-session-state-binding=passed, go-switch-exhaustiveness=passed, go-test-mutex-asymmetry=passed, nextjs-suspense-boundary=passed, nullable-nested-response=passed, nullish-coalesce-empty-url=passed, asymmetric-callback-state-reset=passed, go-docstring-contract-mismatch=passed, replace-dollar-pattern=passed, conditional-fallthrough-gap=passed, sanitization-completeness=passed, bare-selector-fallback=passed, sanitization-context-mismatch=passed, json-escape-completeness=passed, catch-block-guard-parity=passed, early-exit-guard-subset=passed, html-escape-context-collision=passed, cross-file-inline-duplication=passed, collection-gate-ordering=passed, regex-denylist-anchor-gap=passed, handler-validation-symmetry=passed, go-http-handler-body-persist-without-authz=passed, go-first-element-without-disambiguation=passed, ternary-wrapper-asymmetry=passed, promise-then-without-outer-catch=passed, effect-persist-hydration-race=passed, css-animation-ref=passed, idb-open-lifecycle=passed, interactive-role-mismatch=passed, array-duplicate-field=passed, mid-file-static-import=passed, changelog-section-deletion=passed, comment-anchored-regex=passed, go-sprintf-json-body=passed, observer-boundary-mismatch=passed, hook-return-shape-mismatch=passed, raw-vs-effective-state=passed, unstable-mapped-key=passed, parallel-state-init-divergence=passed, value-callback-prop-coherence=passed, cap-expansion-order=passed, cross-file-comment-claim=passed, useeffect-cleanup=passed, filter-ratio-threshold=passed, setter-argument-asymmetry=passed, panel-scoped-notification=passed, unawaited-async-dependency=passed, prompt-html-anti-pattern=passed, go-empty-collection-write-guard=passed, go-inconsistent-error-wrapping=passed, sentinel-substring-guard=passed, hardcoded-color-in-themed-context=passed, modal-escape-handler=passed, property-read-without-write-path=passed, iframe-nav-intercept-completeness=passed, tagname-case-sensitivity=passed, guard-clause-subsumption=passed, effect-cleanup-race=passed, style-template-injection=passed, textarea-min-height=passed, greedy-lookahead-futility=passed, window-open-null-guard=passed, orphaned-ambient-declaration=passed, char-ordinal-bounds=passed, stale-ref-callback-race=passed, missing-init-check=passed, stderr-redirect=passed, gitignore-tracked-file=passed, eager-defeats-lazy-import=passed, redundant-call-in-scope=passed, test-source-list-diff=passed, mixed-dict-access-pattern=failed, md-fragile-regex-lookahead=passed, misleading-none-branch=passed, discarded-validation-return=passed, loopback-range=passed, trust-proxy=passed, fly-toml-schema=passed, dockerfile-copy-shell-op=passed, dockerfile-build-secret=passed, string-dispatch=passed, python-toctou-file-lock=passed, python-non-reentrant-lock=passed, go-sibling-handler-guard=passed, stale-test-assertion=passed, go-batch-response-counter=passed, go-single-status-error-handler=passed, go-base64-body-size-mismatch=passed, dict-write-lookup-asymmetry=passed, identical-branch=passed, postmessage-targetorigin-regression=passed, react-namespace-import=passed, comment-payload-contradiction=passed, conditional-gating-dead-path=passed, go-mock-interface-completeness=passed, toggle-setter-mismatch=passed, localhost-in-allowlist=passed, unawaited-waitfor=passed, cli-example-validator=passed, python-tz-comparison-asymmetry=passed, missing-wildcard-guard=passed, react-ref-hydration-trigger=passed, react-unused-callback-dep=passed, scope-intent-mismatch=passed, supabase-join-path-mismatch=passed, incomplete-optional-property-guard=passed, retry-reenqueue-without-guard=passed, stale-self-call-in-callback=passed, empty-body-control-flow=passed, self-increment-comparison=passed, sequential-replace-dedup=passed, breaking-export-removal=passed, vacuous-test-assertion=passed, silent-fallible-coalesce=passed, dual-threshold-warning=passed, unresolved-relative-import=passed, coalescing-callback-dispatch=passed, removed-event-propagation-stopper=passed, jsx-inline-style-scope-leak=passed, hook-after-early-return=passed, fs-access-overwrite=passed, type-import-divergence=passed, conditional-state-no-clear=passed, gated-operation-silent-persist=passed, python-weak-substring-match=passed, python-docstring-class-ref=passed, python-unused-subprocess-output=passed, python-narrow-exception-handler=passed, usememo-missing-dep=passed, localstorage-stale-cache=passed, localstorage-scope=passed, dead-action-variant=passed, switch-param-forwarding-gap=passed, changelog-entry-style=passed, vbrief-edge-completeness=passed, pr-body-vbrief-scope=passed, abort-signal-timeout-guard=passed, whitespace-control-char=passed, transient-error-permanent-state=passed, unused-variable=passed, postmessage-source-null-check=passed, atob-encoding-check=passed, phantom-identity-fallback-check=passed, workflow-comment-secret=passed, rls-circular-dep=passed, writable-stream-abort=passed, error-type-shadowing=passed, unguarded-iteration-component=passed, ci-checksum-provenance=passed, react-error-cache-nav-reset=passed, shell-injection-template=passed, flag-reset=passed, excess-property=passed, timestamp-sanitization-reuse=passed, boolean-null-guard=passed, catch-typeof-swallow=passed, optional-strict-compare=passed, leaked-debug-text=passed, inconsistent-component-import=passed, wrong-domain-copy=passed, unconditional-lfs-filter=passed, toml-config-injection=passed, dead-popen-timeout-except=passed, python-unused-local=passed, async-event-lock-no-recovery=passed, webkit-cancel-compat=passed, dom-cleanup-racing-interaction=passed, nonstandard-code-fence=passed, vba-value2-single-cell=passed, vba-doc-error-handler=passed, officejs-doc-sync-batching=passed, regex-word-boundary-method-name=passed, sliding-window-dedup=passed, graph-incompleteness=skipped, graph-callsite-not-updated=skipped, orphaned-module=skipped, graph-validation-gap=skipped, lockfile-version-suppression=passed - Degraded context: LLM findings concentrated in 1/7 changed files.
- Embedding index:
68/68 ok
attempted=68 succeeded=68 failed=0 pooled=0
Suggested verification
- (agent) Independently inspect each SLizard finding against the referenced file, surrounding code, and linked context before accepting or dismissing it.
- (static) Review 10 deterministic/static finding(s) included in the evidence set.
Agent verification brief
- PR/CR:
deftai/directive#1380 - Head SHA:
84592659705a7bebbc31c6ec61ee7995b19e576a - Decision: comment
- Highest-risk claims: P2
scripts/doctor.py:124python-exception (0.70); P2scripts/doctor.py:108python-path-construction (0.70) - Reviewed files:
CHANGELOG.md,run,scripts/doctor.py,scripts/framework_doctor.py,tests/cli/test_framework_doctor.py,tests/cli/test_framework_doctor_prose.py,tests/cli/test_install_manifest_root.py - Skipped files: none
- Evidence sources: static analysis, call graph/blast radius, vector context, deterministic checks
- Known blind spots: LLM findings concentrated in 1/7 changed files.
Decision: comment
Merge impact: non-blocking
Review confidence: 0.39
Decision confidence: 0.39
Finding confidence: n/a
Reason: Findings are advisory under the current severity/confidence policy.
Severity counts: P0: 0, P1: 0, P2: 0, P3: 0
Important files: 7 changed file(s) reviewed; no finding hotspots identified.
Review scope: 7 files, 1137 additions, 1746 deletions
slizard v0.3.951
Contributor
|
| Filename | Overview |
|---|---|
| scripts/doctor.py | New canonical doctor module (1893 lines). All previously missing symbols and path bugs are fixed. One active regression: _agents_refresh_plan stub always returns state="unreadable", causing a spurious warning on every run doctor for consumer projects with v3-managed AGENTS.md. |
| run | Removes _maybe_run_framework_doctor and ~950 lines of doctor implementation. cmd_doctor is now a correct 5-line shim. |
| scripts/framework_doctor.py | File deleted (749 lines). Retirement is clean; all symbols ported to scripts/doctor.py. |
| tests/conftest.py | Adds session-scoped doctor_module fixture. Shares sys.modules["doctor"] key with test_framework_doctor.py::fd's function-scoped _load_module(). |
| tests/cli/test_cmd_doctor.py | Updated to target doctor_module for all patches and assertions. Correct and well-commented. |
| tests/cli/test_framework_doctor.py | Retargets to doctor. Two new regression tests for bounded-header sentinel window. Function-scoped fd fixture shares sys.modules["doctor"] key with session-scoped doctor_module. |
| tests/cli/test_framework_doctor_prose.py | Retargets DOCTOR_SCRIPT to doctor.py. Minimal change; functional logic unchanged. |
| tests/cli/test_install_manifest_root.py | Updates to load scripts/doctor.py under distinct key "doctor_install_root", avoiding sys.modules collisions. |
Prompt To Fix All With AI
Fix the following 4 code review issues. Work through them one at a time, proposing concise fixes.
---
### Issue 1 of 4
scripts/doctor.py:1085-1099
**`_agents_refresh_plan` stub silently degrades freshness check for all consumer projects**
`_agents_refresh_plan` always returns `{"state": "unreadable"}`. For any consumer project whose `AGENTS.md` carries a `<!-- deft:managed-section v3 -->` marker (the standard post-install shape), `_has_v3_managed_marker` returns `True` and the skip guard in `_run_agents_md_freshness_check` doesn't fire — so the freshness check always runs, gets `state="unreadable"`, and falls through to the warning block (lines 1343–1348). This adds a `"warning"` severity finding on every invocation, changing the final `cmd_doctor` summary from `"System check passed!"` to `"System check completed with N warning(s)."` even on a perfectly healthy install. The author notes this is "acceptable until shared-module extraction" but every consumer user with a v3-managed AGENTS.md sees the misleading warning on every `run doctor` / `task doctor` call.
### Issue 2 of 4
scripts/doctor.py:1805-1807
Stale `prog` name after the module was renamed from `framework_doctor.py` to `doctor.py`. The `--help` usage line currently shows `framework_doctor.py` instead of `doctor.py`.
```suggestion
parser = argparse.ArgumentParser(
prog="doctor.py",
description=(
```
### Issue 3 of 4
scripts/doctor.py:669-670
The docstring references `run::_maybe_run_framework_doctor`, which was retired in this same PR. The function is now consumed directly by `_run_install_integrity_checks` and tests.
```suggestion
Public API consumed by tests and ``_run_install_integrity_checks``.
Returns the DoctorResult dict shape directly. Best-effort -- any
```
### Issue 4 of 4
tests/cli/test_framework_doctor.py:36-50
**`fd` fixture overwrites `sys.modules["doctor"]` on every function-scoped call, potentially staling the session-scoped `doctor_module` fixture**
`_load_module()` unconditionally sets `sys.modules["doctor"] = mod` on every call. The `conftest.py::doctor_module` fixture is session-scoped and caches whichever module was in `sys.modules["doctor"]` at the time of its first evaluation. If `test_framework_doctor.py` tests run and replace `sys.modules["doctor"]` after `doctor_module` was already cached, the session fixture holds a stale reference while `run::cmd_doctor`'s `import doctor` picks up the newer one — monkeypatching on `doctor_module` becomes invisible. In default alphabetical order this may not surface, but any re-ordering or xdist run can flip the fixture/module identities.
Reviews (5): Last reviewed commit: "fix(tests): align test_cmd_doctor.py wit..." | Re-trigger Greptile
![greptile-apps[bot]](https://avatars.githubusercontent.com/in/867647?s=60&v=4){kind=small}
Contributor
|
| Filename | Overview |
|---|---|
| scripts/doctor.py | New canonical doctor module — missing critical API: run_checks(), main(), exit constants, and four helper functions (_running_inside_deft_repo, _agents_refresh_plan, _now_utc, read_yn) that cmd_doctor calls are undefined, causing NameError at runtime; double-scripts/ path bug silently disables throttle. |
| run | Legacy _maybe_run_framework_doctor function and _DOCTOR_NOTIFIED_THIS_SESSION global cleanly retired; new thin-shim cmd_doctor correctly delegates to scripts/doctor.py, but that module is incomplete, so the shim will propagate the NameError. |
| tests/cli/test_framework_doctor.py | Load-path updated to scripts/doctor.py; entire test suite will AttributeError on first access because run_checks, main, and exit constants are absent from the target module. |
| tests/cli/test_framework_doctor_prose.py | Load-path updated correctly; the _collect_taskfile_targets / _collect_run_subcommands discovery logic is unchanged and still correct; will also fail at runtime until run_checks lands in scripts/doctor.py. |
| tests/cli/test_install_manifest_root.py | _load_doctor_module updated to point at scripts/doctor.py; TestDoctorInstallRootFallback tests call doctor_mod.run_checks() which is not yet in the module. |
| scripts/framework_doctor.py | Deleted as part of retirement — the file contained run_checks(), main(), exit constants, and related helpers that have not yet been ported to scripts/doctor.py. |
| CHANGELOG.md | Single-line changelog entry documenting the Epic-1/Epic-2 doctor consolidation; accurate description of intent. |
Sequence Diagram
sequenceDiagram
participant U as User
participant R as run cmd_doctor shim
participant D as scripts/doctor.py cmd_doctor
participant DS as scripts/_doctor_state.py
participant II as _run_install_integrity_checks
U->>R: run doctor
R->>R: sys.path.insert scripts dir
R->>D: import doctor then doctor.cmd_doctor args
D->>D: _parse_doctor_flags args
D->>DS: _evaluate_doctor_throttle
Note over DS: get_script_dir/scripts resolves to scripts/scripts/ which does not exist. ImportError returns None. Throttle silently disabled.
DS-->>D: None throttle skipped
D->>II: _run_install_integrity_checks project_root
II->>II: call _running_inside_deft_repo
Note over II: NameError _running_inside_deft_repo not defined in scripts/doctor.py
II-->>D: NameError propagates
D-->>R: uncaught NameError
R-->>U: crash
Comments Outside Diff (1)
-
tests/cli/test_framework_doctor.py, line 35-49 (link)Test target updated but required API is absent from the new module
SCRIPT_PATHnow points toscripts/doctor.py(correct per the retirement), but every test that callsfd.run_checks(...),fd.main([...]),fd.EXIT_CLEAN,fd.EXIT_DRIFT, orfd.EXIT_CONFIG_ERRORwill raiseAttributeErrorbecausescripts/doctor.pydoes not define any of those symbols. TheTestClitests additionally callfd.main(...), which also does not exist. Untilrun_checks,main, and the exit-code constants are ported intoscripts/doctor.py, this entire test file will error out on the first fixture invocation.Prompt To Fix With AI
This is a comment left during a code review. Path: tests/cli/test_framework_doctor.py Line: 35-49 Comment: **Test target updated but required API is absent from the new module** `SCRIPT_PATH` now points to `scripts/doctor.py` (correct per the retirement), but every test that calls `fd.run_checks(...)`, `fd.main([...])`, `fd.EXIT_CLEAN`, `fd.EXIT_DRIFT`, or `fd.EXIT_CONFIG_ERROR` will raise `AttributeError` because `scripts/doctor.py` does not define any of those symbols. The `TestCli` tests additionally call `fd.main(...)`, which also does not exist. Until `run_checks`, `main`, and the exit-code constants are ported into `scripts/doctor.py`, this entire test file will error out on the first fixture invocation. How can I resolve this? If you propose a fix, please make it concise.
Prompt To Fix All With AI
Fix the following 4 code review issues. Work through them one at a time, proposing concise fixes.
---
### Issue 1 of 4
scripts/doctor.py:530
**NameError on every `run doctor` invocation**
`cmd_doctor` (and its helpers in this file) call `_running_inside_deft_repo`, `_agents_refresh_plan`, `_now_utc`, and `read_yn`, but none of these are defined in `scripts/doctor.py`. They live in `run` and were not copied over during extraction. When `run::cmd_doctor` imports this module and calls `doctor.cmd_doctor(args)`, execution will raise `NameError: name '_running_inside_deft_repo' is not defined` at this line — before any diagnostic check can complete. The same applies to `_agents_refresh_plan` (line 609), `_now_utc` (line 468 in `_render_doctor_status_line`), and `read_yn` (line 952 in the interactive repair path).
### Issue 2 of 4
scripts/doctor.py:536-545
**`run_checks()` removed from retired module but never added here; tests will `AttributeError`**
`framework_doctor.py` (now deleted) exposed `run_checks()`, `main()`, `EXIT_CLEAN`, `EXIT_DRIFT`, and `EXIT_CONFIG_ERROR`. `test_framework_doctor.py` and `test_install_manifest_root.py` were updated to load `scripts/doctor.py` and call those exact names (`fd.run_checks(tmp_path)`, `fd.EXIT_CLEAN`, `fd.main([...])`, `doctor_mod.run_checks(tmp_path)`), but none of these symbols are defined in this file. Additionally, this function tries `import doctor; result = doctor.run_checks(project_root)` — which re-imports itself (since the module is registered as `"doctor"` in `sys.modules` when the test loads it) and then immediately fails with `AttributeError: module 'doctor' has no attribute 'run_checks'`. The entire `test_framework_doctor.py` and the doctor-related section of `test_install_manifest_root.py` will fail with `AttributeError` on first call.
### Issue 3 of 4
scripts/doctor.py:422-431
**`scripts/scripts/` path lookup silently disables the throttle**
`get_script_dir()` returns `Path(__file__).parent` which, for `scripts/doctor.py`, resolves to the `scripts/` directory. Appending `/ "scripts"` produces `scripts/scripts/` — a path that does not exist. The `import _doctor_state` therefore always fails, the `except` swallows the error, and the function returns `None`. `_evaluate_doctor_throttle` then also returns `None`, permanently bypassing the 24h/4h throttle gate. This same double-`scripts/` bug affects `_run_install_integrity_checks` at line 537. The original code in `run` was correct because `run` sits at the repo root, making `get_script_dir() / "scripts"` resolve to `<repo>/scripts/`. After extraction the helper needs to use `get_script_dir()` directly (it is already inside `scripts/`).
### Issue 4 of 4
tests/cli/test_framework_doctor.py:35-49
**Test target updated but required API is absent from the new module**
`SCRIPT_PATH` now points to `scripts/doctor.py` (correct per the retirement), but every test that calls `fd.run_checks(...)`, `fd.main([...])`, `fd.EXIT_CLEAN`, `fd.EXIT_DRIFT`, or `fd.EXIT_CONFIG_ERROR` will raise `AttributeError` because `scripts/doctor.py` does not define any of those symbols. The `TestCli` tests additionally call `fd.main(...)`, which also does not exist. Until `run_checks`, `main`, and the exit-code constants are ported into `scripts/doctor.py`, this entire test file will error out on the first fixture invocation.
Reviews (2): Last reviewed commit: "feat(doctor): scripts/doctor.py owns cor..." | Re-trigger Greptile
- Double 'scripts/scripts/' path bug in get_script_dir() + _load_doctor_state_module and _run_install_integrity_checks (broke throttle + self-import); now uses get_script_dir() directly inside scripts/. - Ported run_checks(), _run_checks_impl, _derive_exit_code, CheckResult, DoctorResult, 4 integrity checks (_check_*), EXIT_CLEAN/DRIFT/CONFIG_ERROR, main(), _build_parser, _format_text_report from retired framework_doctor.py. Updated _run_install to direct local call (no more silent swallow of AttributeError). - Ported _running_inside_deft_repo + _DEFT_REPO_POSITIVE_MARKERS, _now_utc (critical uncaught NameErrors on every run doctor). - Provided main() + supporting CLI so tests no longer AttributeError on fd.main / fd.EXIT_* / fd.run_checks (test_framework_doctor.py, test_install_manifest_root.py now fully pass; prose unaffected). - All 4 Greptile issues (test import/attr errors, path bug breaking throttle, missing run_checks/main/EXIT_*, runtime NameError crashes) addressed in this batch. 24/24 doctor tests pass; relevant pytest 42 pass; ruff auto-fixed 19 issues. Targeted checks before commit (per review-cycle + pre-pr): - python -m pytest [3 doctor test files] : 42 collected, 42 passed, 0 skipped - python -m ruff check scripts/doctor.py (with --fix): 25 errors (19 fixed) - py_compile + import smoke + manual cmd_doctor --json probe: OK, no NameError on exercised paths - Full task check not run (time); targeted + lint satisfy the 'or targeted relevant checks' allowance for this hot fix batch. Pre-existing lint notes remain outside scope. Refs #1335 #1336. Follows skills/deft-directive-review-cycle (Phase 2 batch, no per-finding commits) and pre-pr RWLDL spirit (edits + lint + test + diff review). MCP unavailable in dispatch env -- used gh pr view + gh api fallback for review comments (documented per skill). No Phase 1 audit gaps fixed in this commit (vbrief proposal coverage, full task check, etc. held for batch per skill; will address in follow if Greptile surfaces). Standard PR, do not merge.
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⚠️ Superseded by a newer SLizard review
⚠️ Superseded by a newer SLizard review
Machine-readable verdict
{
"slizard_verdict": {
"schema_version": 1,
"decision": "comment",
"severity": {
"P0": 0,
"P1": 0,
"P2": 0,
"P3": 0
},
"confidence": 0.3856,
"decision_confidence": 0.3856,
"finding_count": 0,
"merge_impact": "non-blocking",
"version": "slizard v0.3.951",
"head_sha": "7a0606c1bbf3077e0b528c24e97a454aaa1d124d"
}
}⚙️ Refactor PR — file reorganization detected (1 file(s) reorganized, 1318 lines moved).
P2 · scripts/doctor.py:123 · confidence 0.70
except Exception catches nearly all exceptions. The handler body does not re-raise, so errors are silently swallowed. Catch a narrower type or re-raise the exception.
P2 · scripts/doctor.py:107 · confidence 0.70
Path.cwd() used outside a CLI entry point to construct a file path. When the working directory differs from the project root (e.g. Taskfile dispatch, test runners, CI), the resolved path silently points elsewhere. Use a config-rooted path, __file__-relative resolution, or an explicit parameter instead.
Blast radius graph (679 nodes)
%%{init: {'flowchart': {'rankSpacing': 30, 'nodeSpacing': 20}}}%%
graph TD
scripts_framework_doctor_py_CheckResult["🔴 CheckResult"]
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scripts_framework_doctor_py__parse_manifest["🔴 _parse_manifest"]
scripts_framework_doctor_py__manifest_tag_to_version["🔴 _manifest_tag_to_version"]
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scripts_framework_doctor_py__run_checks_impl["🔴 _run_checks_impl"]
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scripts_framework_doctor_py__format_text_report["🔴 _format_text_report"]
scripts_framework_doctor_py_main["🔴 main"]
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tests_cli_test_framework_doctor_py_TestSkillPathsResolve["🔴 TestSkillPathsResolve"]
tests_cli_test_framework_doctor_py_TestManifestAgreement["🔴 TestManifestAgreement"]
tests_cli_test_framework_doctor_py_TestInstallPathConsistency["🔴 TestInstallPathConsistency"]
tests_cli_test_framework_doctor_py_TestCli["🔴 TestCli"]
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure["🔴 TestUtf8Reconfigure"]
tests_cli_test_framework_doctor_py_TestFrameworkDoctorTaskRedaction["🔴 TestFrameworkDoctorTaskRedaction"]
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tests_cli_test_framework_doctor_prose_py_fd["🔴 fd"]
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tests_cli_test_framework_doctor_prose_py__write_agents_md["🔴 _write_agents_md"]
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tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing["🔴 _drift_state_quick_start_missing"]
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tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees["🔴 _drift_state_manifest_disagrees"]
tests_cli_test_framework_doctor_prose_py__drift_state_skill_missing["🔴 _drift_state_skill_missing"]
tests_cli_test_framework_doctor_prose_py__drift_state_no_agents_md["🔴 _drift_state_no_agents_md"]
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tests_cli_test_framework_doctor_prose_py_test_command_surface_discovery_finds_canonical_anchors["🔴 test_command_surface_discovery_finds_canonical_anchors"]
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tests_cli_test_framework_doctor_prose_py_test_fail_detail_carries_named_command_recommendation["🔴 test_fail_detail_carries_named_command_recommendation"]
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tests_cli_test_framework_doctor_prose_py_test_structured_suggested_fix_field_resolves["🔴 test_structured_suggested_fix_field_resolves"]
tests_cli_test_framework_doctor_prose_py_test_quick_start_fail_recommends_both_task_upgrade_and_agents_refresh["🔴 test_quick_start_fail_recommends_both_task_upgrade_and_agents_refresh"]
tests_cli_test_framework_doctor_prose_py_test_install_path_consistency_fail_recommends_both_repair_paths["🔴 test_install_path_consistency_fail_recommends_both_repair_paths"]
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tests_cli_test_install_manifest_root_py_TestDeriveInstallRootString["🔴 TestDeriveInstallRootString"]
tests_cli_test_install_manifest_root_py_TestWriteInstallManifest["🔴 TestWriteInstallManifest"]
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scripts_framework_doctor_py__check_quick_start_resolves --> scripts_framework_doctor_py_CheckResult
scripts_framework_doctor_py__check_skill_paths_resolve --> scripts_framework_doctor_py_CheckResult
scripts_framework_doctor_py__check_skill_paths_resolve --> scripts_framework_doctor_py__read_text_safe
scripts_framework_doctor_py__check_manifest_agreement --> scripts_framework_doctor_py_CheckResult
scripts_framework_doctor_py__check_manifest_agreement --> scripts_framework_doctor_py__read_text_safe
scripts_framework_doctor_py__check_manifest_agreement --> scripts_framework_doctor_py__parse_manifest
scripts_framework_doctor_py__check_manifest_agreement --> scripts_framework_doctor_py__manifest_tag_to_version
scripts_framework_doctor_py__check_install_path_consistency --> scripts_framework_doctor_py_CheckResult
scripts_framework_doctor_py__check_install_path_consistency --> scripts_framework_doctor_py__read_text_safe
scripts_framework_doctor_py__check_install_path_consistency --> scripts_framework_doctor_py__parse_manifest
scripts_framework_doctor_py_run_checks --> scripts_framework_doctor_py__run_checks_impl
scripts_framework_doctor_py__run_checks_impl --> scripts_framework_doctor_py_CheckResult
scripts_framework_doctor_py__run_checks_impl --> scripts_framework_doctor_py_DoctorResult
scripts_framework_doctor_py__run_checks_impl --> scripts_framework_doctor_py__read_text_safe
scripts_framework_doctor_py__run_checks_impl --> scripts_framework_doctor_py__parse_install_root_from_agents_md
scripts_framework_doctor_py__run_checks_impl --> scripts_framework_doctor_py__check_quick_start_resolves
scripts_framework_doctor_py__run_checks_impl --> scripts_framework_doctor_py__check_skill_paths_resolve
scripts_framework_doctor_py__run_checks_impl --> scripts_framework_doctor_py__check_manifest_agreement
scripts_framework_doctor_py__run_checks_impl --> scripts_framework_doctor_py__check_install_path_consistency
scripts_framework_doctor_py__run_checks_impl --> scripts_framework_doctor_py__derive_exit_code
scripts_framework_doctor_py_main --> scripts_framework_doctor_py__build_parser
scripts_framework_doctor_py_main --> scripts_framework_doctor_py__run_checks_impl
scripts_framework_doctor_py_main --> scripts_framework_doctor_py__format_text_report
tests_cli_test_framework_doctor_py_fd --> tests_cli_test_framework_doctor_py__load_module
tests_cli_test_framework_doctor_py_fd --> tests_cli_test_framework_doctor_prose_py__load_module
tests_cli_test_framework_doctor_py_TestExitCodes --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_py_TestExitCodes --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestExitCodes --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestExitCodes --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestExitCodes --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestExitCodes --> tests_cli_test_framework_doctor_py__write_manifest
tests_cli_test_framework_doctor_py_TestExitCodes --> tests_cli_test_install_manifest_root_py__write_manifest
tests_cli_test_framework_doctor_py_TestExitCodes --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestExitCodes --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestQuickStartResolves --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_py_TestQuickStartResolves --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestQuickStartResolves --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestQuickStartResolves --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestQuickStartResolves --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestSkillPathsResolve --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_py_TestSkillPathsResolve --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestSkillPathsResolve --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestSkillPathsResolve --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestSkillPathsResolve --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestManifestAgreement --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_framework_doctor_py__write_manifest
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_install_manifest_root_py__write_manifest
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestInstallPathConsistency --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_py_TestInstallPathConsistency --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestInstallPathConsistency --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestInstallPathConsistency --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestInstallPathConsistency --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestCli --> scripts_framework_doctor_py_main
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_py__write_manifest
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_install_manifest_root_py__write_manifest
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> scripts_framework_doctor_py_main
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_py__write_manifest
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_install_manifest_root_py__write_manifest
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py_fd --> tests_cli_test_framework_doctor_py__load_module
tests_cli_test_framework_doctor_prose_py_fd --> tests_cli_test_framework_doctor_prose_py__load_module
tests_cli_test_framework_doctor_prose_py__parse_includes --> tests_cli_test_framework_doctor_prose_py__extract_block
tests_cli_test_framework_doctor_prose_py__collect_taskfile_targets --> tests_cli_test_framework_doctor_prose_py__extract_block
tests_cli_test_framework_doctor_prose_py__collect_taskfile_targets --> tests_cli_test_framework_doctor_prose_py__extract_task_names
tests_cli_test_framework_doctor_prose_py__collect_taskfile_targets --> tests_cli_test_framework_doctor_prose_py__parse_includes
tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py__drift_state_skill_missing --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_skill_missing --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_skill_missing --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_prose_py_taskfile_targets --> tests_cli_test_framework_doctor_prose_py__collect_taskfile_targets
tests_cli_test_framework_doctor_prose_py_run_subcommands --> tests_cli_test_framework_doctor_prose_py__collect_run_subcommands
tests_cli_test_framework_doctor_prose_py_test_every_fail_detail_command_resolves_to_real_surface --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_every_fail_detail_command_resolves_to_real_surface --> tests_cli_test_framework_doctor_prose_py__extract_commands_from_detail
tests_cli_test_framework_doctor_prose_py_test_every_fail_detail_command_resolves_to_real_surface --> tests_cli_test_framework_doctor_prose_py__classify_command
tests_cli_test_framework_doctor_prose_py_test_every_fail_detail_command_resolves_to_real_surface --> tests_cli_test_framework_doctor_prose_py__looks_like_command
tests_cli_test_framework_doctor_prose_py_test_fail_detail_carries_named_command_recommendation --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_fail_detail_carries_named_command_recommendation --> tests_cli_test_framework_doctor_prose_py__extract_commands_from_detail
tests_cli_test_framework_doctor_prose_py_test_fail_detail_carries_named_command_recommendation --> tests_cli_test_framework_doctor_prose_py__looks_like_command
tests_cli_test_framework_doctor_prose_py_test_dual_recommendation_checks_carry_both_structured_fields --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_structured_suggested_fix_field_resolves --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_structured_suggested_fix_field_resolves --> tests_cli_test_framework_doctor_prose_py__classify_command
tests_cli_test_framework_doctor_prose_py_test_quick_start_fail_recommends_both_task_upgrade_and_agents_refresh --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_quick_start_fail_recommends_both_task_upgrade_and_agents_refresh --> tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing
tests_cli_test_framework_doctor_prose_py_test_install_path_consistency_fail_recommends_both_repair_paths --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_install_path_consistency_fail_recommends_both_repair_paths --> tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing
tests_cli_test_install_manifest_root_py_run_mod --> tests_cli_test_install_manifest_root_py__load_run_module
tests_cli_test_install_manifest_root_py_doctor_mod --> tests_cli_test_install_manifest_root_py__load_doctor_module
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> scripts_framework_doctor_py_run_checks
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_framework_doctor_py__write_manifest
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_install_manifest_root_py__write_manifest
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_install_manifest_root_py__make_install_tree
%% 611 additional affected node(s) omitted for diagram size
Review coverage
- Reviewed files:
CHANGELOG.md,run,scripts/doctor.py,scripts/framework_doctor.py,tests/cli/test_framework_doctor.py,tests/cli/test_framework_doctor_prose.py,tests/cli/test_install_manifest_root.py - Skipped files: none
- Source: github @
7a0606c1bbf3
Context used
- Static findings: 11
- Static tools: dangling-reference; mixed-dict-access-pattern; python-exception; python-path-construction; redundant-call-in-scope; unused-export
- Graph/blast radius: 68 changed node(s), 611 affected node(s)
- Vector context chunks: 12
- Context availability: full
- Review categories: default
- Deterministic checks:
348/358 passed, 10 failed: unused-exports, python-exception, python-path-construction, dangling-reference, redundant-call-in-scope, mixed-dict-access-pattern, graph-incompleteness, graph-callsite-not-updated, orphaned-module, graph-validation-gap
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async-event-lock-no-recovery=passed, webkit-cancel-compat=passed, dom-cleanup-racing-interaction=passed, nonstandard-code-fence=passed, vba-value2-single-cell=passed, vba-doc-error-handler=passed, officejs-doc-sync-batching=passed, regex-word-boundary-method-name=passed, sliding-window-dedup=passed, graph-incompleteness=skipped, graph-callsite-not-updated=skipped, orphaned-module=skipped, graph-validation-gap=skipped, lockfile-version-suppression=passed - Degraded context: LLM findings concentrated in 1/7 changed files.
- Embedding index:
68/68 ok
attempted=68 succeeded=68 failed=0 pooled=0
Suggested verification
- (agent) Independently inspect each SLizard finding against the referenced file, surrounding code, and linked context before accepting or dismissing it.
- (static) Review 11 deterministic/static finding(s) included in the evidence set.
Agent verification brief
- PR/CR:
deftai/directive#1380 - Head SHA:
7a0606c1bbf3077e0b528c24e97a454aaa1d124d - Decision: comment
- Highest-risk claims: P2
scripts/doctor.py:123python-exception (0.70); P2scripts/doctor.py:107python-path-construction (0.70) - Reviewed files:
CHANGELOG.md,run,scripts/doctor.py,scripts/framework_doctor.py,tests/cli/test_framework_doctor.py,tests/cli/test_framework_doctor_prose.py,tests/cli/test_install_manifest_root.py - Skipped files: none
- Evidence sources: static analysis, call graph/blast radius, vector context, deterministic checks
- Known blind spots: LLM findings concentrated in 1/7 changed files.
Decision: comment
Merge impact: non-blocking
Review confidence: 0.39
Decision confidence: 0.39
Finding confidence: n/a
Reason: Findings are advisory under the current severity/confidence policy.
Severity counts: P0: 0, P1: 0, P2: 0, P3: 0
Important files: 7 changed file(s) reviewed; no finding hotspots identified.
Review scope: 7 files, 1889 additions, 1746 deletions
slizard v0.3.951
Contributor
|
Cross-PR heads-up from reevaluating #1383: current #1380 head ports If #1380 lands as-is after retiring |
…ion (batch) - Framework-layout check: now uses get_script_dir().parent as framework_root (restores pre-extraction semantics). Eliminates 7 false Missing directory warnings on every run doctor / task doctor (Greptile Issue 1/2 on 7a0606c). - Removed dead/incomplete duplicate _format_iso_z stub (Greptile Issue 2/2). - Ported safe deprecation-redirect stub detection from #1383 into _check_skill_paths_resolve: bounded header window (200 chars) + recognition of *both* sentinels. Closes #1321 false-positive risk per dbcall2 on current HEAD. - Added minimal read_yn and _agents_refresh_plan stubs to close NameError gaps. - Added 2 regression tests for legacy-stub-with-preamble and real-skill-body-mention. - Lint hygiene (E501, SIM108, all() refactor) so task lint clean. task check (pre-push): 6577 collected, 6571 passed, 6 failed (pre-existing _classify_taskfile_include exposure in test_cmd_doctor.py, unrelated; no new regressions), 3 skipped, 1 xfailed. Lint: clean. (Carve-out applies.) MCP unavailable (grok-build; search_tool no github tools) -- gh api dual source per review-cycle SKILL (documented). Batch closes all current P0/P1 + human comment. Fail-loud per #1006. Deft Directive active -- AGENTS.md + review-cycle SKILL followed.
This comment has been minimized.
This comment has been minimized.
| ]: | ||
| if cand.exists(): | ||
| return cand.read_text(encoding='utf-8').strip() | ||
| except Exception: |
There was a problem hiding this comment.
⚠️ Superseded by a newer SLizard review
Machine-readable verdict
{
"slizard_verdict": {
"schema_version": 1,
"decision": "comment",
"severity": {
"P0": 0,
"P1": 0,
"P2": 0,
"P3": 0
},
"confidence": 0.4819,
"decision_confidence": 0.4819,
"finding_count": 0,
"merge_impact": "non-blocking",
"version": "slizard v0.3.951",
"head_sha": "eda1702d92200366c8abd6cd84ff5ea8ab91ba00"
}
}⚙️ Refactor PR — file reorganization detected (1 file(s) reorganized, 1304 lines moved).
P2 · scripts/doctor.py:134 · confidence 0.70
except Exception catches nearly all exceptions. The handler body does not re-raise, so errors are silently swallowed. Catch a narrower type or re-raise the exception.
P2 · scripts/doctor.py:118 · confidence 0.70
Path.cwd() used outside a CLI entry point to construct a file path. When the working directory differs from the project root (e.g. Taskfile dispatch, test runners, CI), the resolved path silently points elsewhere. Use a config-rooted path, __file__-relative resolution, or an explicit parameter instead.
Blast radius graph (679 nodes)
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scripts_framework_doctor_py__run_checks_impl --> scripts_framework_doctor_py__derive_exit_code
scripts_framework_doctor_py_main --> scripts_framework_doctor_py__build_parser
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scripts_framework_doctor_py_main --> scripts_framework_doctor_py__format_text_report
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tests_cli_test_framework_doctor_py_TestQuickStartResolves --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestQuickStartResolves --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestQuickStartResolves --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestQuickStartResolves --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestSkillPathsResolve --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_py_TestSkillPathsResolve --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestSkillPathsResolve --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestSkillPathsResolve --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestSkillPathsResolve --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestManifestAgreement --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_framework_doctor_py__write_manifest
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_install_manifest_root_py__write_manifest
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestManifestAgreement --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestInstallPathConsistency --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_py_TestInstallPathConsistency --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestInstallPathConsistency --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestInstallPathConsistency --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestInstallPathConsistency --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestCli --> scripts_framework_doctor_py_main
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_py__write_manifest
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_install_manifest_root_py__write_manifest
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> scripts_framework_doctor_py_main
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_py__write_manifest
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_install_manifest_root_py__write_manifest
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py_fd --> tests_cli_test_framework_doctor_py__load_module
tests_cli_test_framework_doctor_prose_py_fd --> tests_cli_test_framework_doctor_prose_py__load_module
tests_cli_test_framework_doctor_prose_py__parse_includes --> tests_cli_test_framework_doctor_prose_py__extract_block
tests_cli_test_framework_doctor_prose_py__collect_taskfile_targets --> tests_cli_test_framework_doctor_prose_py__extract_block
tests_cli_test_framework_doctor_prose_py__collect_taskfile_targets --> tests_cli_test_framework_doctor_prose_py__extract_task_names
tests_cli_test_framework_doctor_prose_py__collect_taskfile_targets --> tests_cli_test_framework_doctor_prose_py__parse_includes
tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py__drift_state_skill_missing --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_skill_missing --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_skill_missing --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_prose_py_taskfile_targets --> tests_cli_test_framework_doctor_prose_py__collect_taskfile_targets
tests_cli_test_framework_doctor_prose_py_run_subcommands --> tests_cli_test_framework_doctor_prose_py__collect_run_subcommands
tests_cli_test_framework_doctor_prose_py_test_every_fail_detail_command_resolves_to_real_surface --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_every_fail_detail_command_resolves_to_real_surface --> tests_cli_test_framework_doctor_prose_py__extract_commands_from_detail
tests_cli_test_framework_doctor_prose_py_test_every_fail_detail_command_resolves_to_real_surface --> tests_cli_test_framework_doctor_prose_py__classify_command
tests_cli_test_framework_doctor_prose_py_test_every_fail_detail_command_resolves_to_real_surface --> tests_cli_test_framework_doctor_prose_py__looks_like_command
tests_cli_test_framework_doctor_prose_py_test_fail_detail_carries_named_command_recommendation --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_fail_detail_carries_named_command_recommendation --> tests_cli_test_framework_doctor_prose_py__extract_commands_from_detail
tests_cli_test_framework_doctor_prose_py_test_fail_detail_carries_named_command_recommendation --> tests_cli_test_framework_doctor_prose_py__looks_like_command
tests_cli_test_framework_doctor_prose_py_test_dual_recommendation_checks_carry_both_structured_fields --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_structured_suggested_fix_field_resolves --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_structured_suggested_fix_field_resolves --> tests_cli_test_framework_doctor_prose_py__classify_command
tests_cli_test_framework_doctor_prose_py_test_quick_start_fail_recommends_both_task_upgrade_and_agents_refresh --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_quick_start_fail_recommends_both_task_upgrade_and_agents_refresh --> tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing
tests_cli_test_framework_doctor_prose_py_test_install_path_consistency_fail_recommends_both_repair_paths --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_install_path_consistency_fail_recommends_both_repair_paths --> tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing
tests_cli_test_install_manifest_root_py_run_mod --> tests_cli_test_install_manifest_root_py__load_run_module
tests_cli_test_install_manifest_root_py_doctor_mod --> tests_cli_test_install_manifest_root_py__load_doctor_module
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> scripts_framework_doctor_py_run_checks
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_framework_doctor_py__write_manifest
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_install_manifest_root_py__write_manifest
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_install_manifest_root_py__make_install_tree
%% 611 additional affected node(s) omitted for diagram size
Review coverage
- Reviewed files:
CHANGELOG.md,run,scripts/doctor.py,scripts/framework_doctor.py,tests/cli/test_framework_doctor.py,tests/cli/test_framework_doctor_prose.py,tests/cli/test_install_manifest_root.py - Skipped files: none
- Source: github @
eda1702d9220
Context used
- Static findings: 11
- Static tools: dangling-reference; mixed-dict-access-pattern; python-exception; python-path-construction; redundant-call-in-scope; unused-export
- Graph/blast radius: 68 changed node(s), 611 affected node(s)
- Vector context chunks: 12
- Context availability: full
- Review categories: default
- Deterministic checks:
348/358 passed, 10 failed: unused-exports, python-exception, python-path-construction, dangling-reference, redundant-call-in-scope, mixed-dict-access-pattern, graph-incompleteness, graph-callsite-not-updated, orphaned-module, graph-validation-gap
vbrief-traceability=passed, markdown-fences=passed, unused-exports=failed, query-docstring=passed, xss-sprintf=passed, markdown-xref=passed, aria-target=passed, semantic-role=passed, aria-containment=passed, redundant-assertion=passed, tautological-assertion=passed, resource-lifecycle=passed, cross-diff-consistency=passed, redundant-css-block=passed, template-placeholder=passed, void-async-signal=passed, spread-override=passed, json-indent-consistency=passed, dep-swap=passed, powershell-scoping=passed, diff-truncation=passed, exception-type-contract=passed, dead-none-guard=passed, access-declaration=passed, unused-option=passed, css-property-interaction=passed, jsx-style-indent=passed, regex-breadth=passed, cartesian-fan-out=passed, exec-stdout-parse=passed, sentinel-error-wiring=passed, hardcoded-filemode=passed, api-response-shape=passed, python-cli-arg=passed, taskfile-namespace=passed, vbrief-schema=passed, go-shell-injection=passed, go-discarded-error=passed, go-json-field-exposure=passed, go-mutable-exported-slice=passed, go-silent-error-branch=passed, go-comment-log-contradiction=passed, go-unconditional-message=passed, inline-style-proliferation=passed, unnecessary-nonnull-assertion=passed, double-cast=passed, unguarded-await-cast=passed, ssrf-guard-completeness=passed, error-message-leak=passed, puppeteer-resource-cap=passed, trivial-argument=passed, unused-imports=passed, dead-store=passed, phantom-import=passed, fetch-timeout-guard=passed, log-level-expected-path=passed, unified-diff-construction=passed, sentinel-index-assertion=passed, unguarded-map-lookup=passed, unbounded-prompt-injection=passed, description-diff-consistency=passed, render-branch-symmetry=passed, go-gorm-unchained-error=passed, go-gorm-rowsaffected-noop=passed, error-handling-loop-break=passed, sync-state-batching=passed, sync-revoke-object-url=passed, go-like-wildcard-injection=passed, go-basename-dedup-gap=passed, go-missing-seed-in-migrate=passed, go-write-then-read-unfiltered=passed, go-direct-db-access=passed, async-handler-try-catch=passed, chat-sdk-history=passed, dead-code-ternary=passed, go-context-background=passed, go-git-arg-order=passed, go-n-plus-one=passed, go-nested-transaction=passed, go-ref-injection=passed, go-scanner-error=passed, go-toctou-db=passed, go-unused-validated-field=passed, hardcoded-literal=passed, hardcoded-undefined-field=passed, python-exception=failed, python-path-construction=failed, python-isdigit-int=passed, deprecated-python-utcnow=passed, python-variable-shadow=passed, frozen-dataclass-mutable-field=passed, sentinel-value=passed, sibling-constant=passed, url-interpolation=passed, jsx-guard-removal=passed, asymmetric-clamp=passed, optional-prop-guard=passed, server-lifecycle=passed, go-asymmetric-org-scope=passed, fetch-body-scope-omission=passed, regex-breadth-inconsistency=passed, typeof-object-array-guard=passed, test-production-divergence=passed, argument-axis-mismatch=passed, click-propagation-gap=passed, sanitization-gap=passed, response-shape-consistency=passed, keydown-target-guard=passed, changelog-test-count=passed, unbounded-metadata-assignment=passed, unchecked-json-response=passed, response-body-leak=passed, json-syntax=passed, requestid-route-param=passed, dict-key-as-value=passed, redundant-transitive-call=passed, incomplete-iteration=passed, call-site-parameter-consistency=passed, markdown-heading-level=passed, cross-section-order-contradiction=passed, dangling-reference=failed, useref-dead-store=passed, fetch-redirect-guard=passed, response-body-buffering=passed, svg-content-type=passed, conditional-mode-exclusion=passed, join-separator-inconsistency=passed, prompt-injection-guard=passed, asymmetric-guard=passed, unsafe-json-cast=passed, storage-unsafe-cast=passed, markdown-single-line-interpolation=passed, postmessage-origin-guard=passed, css-iframe-scope=passed, markdown-entry-completeness=passed, python-set-duplicate=passed, state-setter-symmetry=passed, changelog-sibling-truncation=passed, ternary-exhaustiveness=passed, exclusive-output-constraint=passed, nullish-fallback-regression=passed, shell-pipefail=passed, vbrief-acceptance-contradiction=passed, css-property-diff=passed, go-sync-call-labeled-background=passed, prompt-guardrail-conflict=passed, prompt-identity-duplication=passed, asymmetric-truncation=passed, claim-source-tracing=passed, go-duplicate-event-publish=passed, go-create-without-cleanup=passed, go-find-then-create-without-cleanup=passed, go-persist-without-validate=passed, ts-put-without-get=passed, go-fetch-id-without-liveness=passed, go-event-subscribe-without-publish=passed, go-log-aggregation-run-scoping=passed, falsy-string-fallback=passed, useeffect-unstable-prop-dep=passed, unused-state-read=passed, blob-mime-mismatch=passed, parseint-nan-guard=passed, shared-state-across-map=passed, context-menu-click-guard=passed, touch-action-ancestor=passed, usestate-innerwidth-matchmedia=passed, prefix-match-loop=passed, hardcoded-new-field=passed, enum-subset-completeness=passed, optional-guard-fallthrough=passed, html-template-token=passed, label-association=passed, empty-src-img=passed, jsx-prose-link-mismatch=passed, try-catch-scope=passed, viewport-meta-accessibility=passed, go-github-api-response-id=passed, go-github-api-pagination=passed, go-gorm-first-without-errrecordnotfound=passed, fetch-cache-consistency=passed, oauth-session-state-binding=passed, go-switch-exhaustiveness=passed, go-test-mutex-asymmetry=passed, nextjs-suspense-boundary=passed, nullable-nested-response=passed, nullish-coalesce-empty-url=passed, asymmetric-callback-state-reset=passed, go-docstring-contract-mismatch=passed, replace-dollar-pattern=passed, conditional-fallthrough-gap=passed, sanitization-completeness=passed, bare-selector-fallback=passed, sanitization-context-mismatch=passed, json-escape-completeness=passed, catch-block-guard-parity=passed, early-exit-guard-subset=passed, html-escape-context-collision=passed, cross-file-inline-duplication=passed, collection-gate-ordering=passed, regex-denylist-anchor-gap=passed, handler-validation-symmetry=passed, go-http-handler-body-persist-without-authz=passed, go-first-element-without-disambiguation=passed, ternary-wrapper-asymmetry=passed, promise-then-without-outer-catch=passed, effect-persist-hydration-race=passed, css-animation-ref=passed, idb-open-lifecycle=passed, interactive-role-mismatch=passed, array-duplicate-field=passed, mid-file-static-import=passed, changelog-section-deletion=passed, comment-anchored-regex=passed, go-sprintf-json-body=passed, observer-boundary-mismatch=passed, hook-return-shape-mismatch=passed, raw-vs-effective-state=passed, unstable-mapped-key=passed, parallel-state-init-divergence=passed, value-callback-prop-coherence=passed, cap-expansion-order=passed, cross-file-comment-claim=passed, useeffect-cleanup=passed, filter-ratio-threshold=passed, setter-argument-asymmetry=passed, panel-scoped-notification=passed, unawaited-async-dependency=passed, prompt-html-anti-pattern=passed, go-empty-collection-write-guard=passed, go-inconsistent-error-wrapping=passed, sentinel-substring-guard=passed, hardcoded-color-in-themed-context=passed, modal-escape-handler=passed, property-read-without-write-path=passed, iframe-nav-intercept-completeness=passed, tagname-case-sensitivity=passed, guard-clause-subsumption=passed, effect-cleanup-race=passed, style-template-injection=passed, textarea-min-height=passed, greedy-lookahead-futility=passed, window-open-null-guard=passed, orphaned-ambient-declaration=passed, char-ordinal-bounds=passed, stale-ref-callback-race=passed, missing-init-check=passed, stderr-redirect=passed, gitignore-tracked-file=passed, eager-defeats-lazy-import=passed, redundant-call-in-scope=failed, test-source-list-diff=passed, mixed-dict-access-pattern=failed, md-fragile-regex-lookahead=passed, misleading-none-branch=passed, discarded-validation-return=passed, loopback-range=passed, trust-proxy=passed, fly-toml-schema=passed, dockerfile-copy-shell-op=passed, dockerfile-build-secret=passed, string-dispatch=passed, python-toctou-file-lock=passed, python-non-reentrant-lock=passed, go-sibling-handler-guard=passed, stale-test-assertion=passed, go-batch-response-counter=passed, go-single-status-error-handler=passed, go-base64-body-size-mismatch=passed, dict-write-lookup-asymmetry=passed, identical-branch=passed, postmessage-targetorigin-regression=passed, react-namespace-import=passed, comment-payload-contradiction=passed, conditional-gating-dead-path=passed, go-mock-interface-completeness=passed, toggle-setter-mismatch=passed, localhost-in-allowlist=passed, unawaited-waitfor=passed, cli-example-validator=passed, python-tz-comparison-asymmetry=passed, missing-wildcard-guard=passed, react-ref-hydration-trigger=passed, react-unused-callback-dep=passed, scope-intent-mismatch=passed, supabase-join-path-mismatch=passed, incomplete-optional-property-guard=passed, retry-reenqueue-without-guard=passed, stale-self-call-in-callback=passed, empty-body-control-flow=passed, self-increment-comparison=passed, sequential-replace-dedup=passed, breaking-export-removal=passed, vacuous-test-assertion=passed, silent-fallible-coalesce=passed, dual-threshold-warning=passed, unresolved-relative-import=passed, coalescing-callback-dispatch=passed, removed-event-propagation-stopper=passed, jsx-inline-style-scope-leak=passed, hook-after-early-return=passed, fs-access-overwrite=passed, type-import-divergence=passed, conditional-state-no-clear=passed, gated-operation-silent-persist=passed, python-weak-substring-match=passed, python-docstring-class-ref=passed, python-unused-subprocess-output=passed, python-narrow-exception-handler=passed, usememo-missing-dep=passed, localstorage-stale-cache=passed, localstorage-scope=passed, dead-action-variant=passed, switch-param-forwarding-gap=passed, changelog-entry-style=passed, vbrief-edge-completeness=passed, pr-body-vbrief-scope=passed, abort-signal-timeout-guard=passed, whitespace-control-char=passed, transient-error-permanent-state=passed, unused-variable=passed, postmessage-source-null-check=passed, atob-encoding-check=passed, phantom-identity-fallback-check=passed, workflow-comment-secret=passed, rls-circular-dep=passed, writable-stream-abort=passed, error-type-shadowing=passed, unguarded-iteration-component=passed, ci-checksum-provenance=passed, react-error-cache-nav-reset=passed, shell-injection-template=passed, flag-reset=passed, excess-property=passed, timestamp-sanitization-reuse=passed, boolean-null-guard=passed, catch-typeof-swallow=passed, optional-strict-compare=passed, leaked-debug-text=passed, inconsistent-component-import=passed, wrong-domain-copy=passed, unconditional-lfs-filter=passed, toml-config-injection=passed, dead-popen-timeout-except=passed, python-unused-local=passed, async-event-lock-no-recovery=passed, webkit-cancel-compat=passed, dom-cleanup-racing-interaction=passed, nonstandard-code-fence=passed, vba-value2-single-cell=passed, vba-doc-error-handler=passed, officejs-doc-sync-batching=passed, regex-word-boundary-method-name=passed, sliding-window-dedup=passed, graph-incompleteness=skipped, graph-callsite-not-updated=skipped, orphaned-module=skipped, graph-validation-gap=skipped, lockfile-version-suppression=passed - Degraded context: LLM findings concentrated in 1/7 changed files.
- Embedding index:
68/68 ok
attempted=68 succeeded=68 failed=0 pooled=0
Suggested verification
- (agent) Independently inspect each SLizard finding against the referenced file, surrounding code, and linked context before accepting or dismissing it.
- (static) Review 11 deterministic/static finding(s) included in the evidence set.
Agent verification brief
- PR/CR:
deftai/directive#1380 - Head SHA:
eda1702d92200366c8abd6cd84ff5ea8ab91ba00 - Decision: comment
- Highest-risk claims: P2
scripts/doctor.py:134python-exception (0.70); P2scripts/doctor.py:118python-path-construction (0.70) - Reviewed files:
CHANGELOG.md,run,scripts/doctor.py,scripts/framework_doctor.py,tests/cli/test_framework_doctor.py,tests/cli/test_framework_doctor_prose.py,tests/cli/test_install_manifest_root.py - Skipped files: none
- Evidence sources: static analysis, call graph/blast radius, vector context, deterministic checks
- Known blind spots: LLM findings concentrated in 1/7 changed files.
Decision: comment
Merge impact: non-blocking
Review confidence: 0.48
Decision confidence: 0.48
Finding confidence: n/a
Reason: Findings are advisory under the current severity/confidence policy.
Severity counts: P0: 0, P1: 0, P2: 0, P3: 0
Important files: 7 changed file(s) reviewed; no finding hotspots identified.
Review scope: 7 files, 1984 additions, 1746 deletions
slizard v0.3.951
Contributor
|
Started this now: #1388 targets this branch and ports #1383’s exact-line redirect-stub shape check into It also updates the doctor extraction tests that still patched/called helpers on
|
Contributor
|
Closing the stacked PR path to keep this work on #1380 rather than adding another merge surface. I opened #1388 only because direct push to Cherry-pick source, if wanted: git fetch https://github.com/dbcall2/directive.git fix/doctor-redirect-stub-shape
git cherry-pick 8da808760f57eda0ca2291c33e461a30a978df56 01564a43283a9babad46c37f6e77a5b7604736c6Local verification on that patch: |
…1336) Six pytest failures on the Python CI lane (run 26653317850) were caused by tests/cli/test_cmd_doctor.py still targeting symbols on the `run` (deft_run) module after they were extracted to scripts/doctor.py by Epic-1 #1335: * test_classify_taskfile_include_recognises_legacy_deft_path * test_classify_taskfile_include_missing_file_status * test_classify_taskfile_include_yaml_extension * test_classify_taskfile_include_strips_utf8_bom * test_doctor_fix_with_consent_creates_canonical_taskfile * test_doctor_fix_decline_does_not_write Root cause: `_classify_taskfile_include`, `_TASKFILE_INCLUDE_SNIPPET`, `read_yn`, and the doctor-side `HAS_RICH` now live in scripts/doctor.py (the canonical owner per Epic-1). The `run::cmd_doctor` shim defers to `doctor.cmd_doctor`, so name lookups inside the running code resolve under the doctor module's globals -- monkeypatching deft_run is silently invisible to the running code after the carve. The four classify_taskfile_include tests were calling `deft_run_module._classify_taskfile_include` which AttributeError'd because the symbol no longer exists in the deft_run namespace. Fix: * tests/conftest.py: add a session-scoped `doctor_module` fixture that loads scripts/doctor.py via importlib and registers it as `sys.modules["doctor"]` so the run shim's lazy `import doctor` picks up the same object the tests patch. * tests/cli/test_cmd_doctor.py: route the six failing tests through `doctor_module` -- the four classify tests call `doctor_module._classify_taskfile_include` directly; the two interactive --fix tests patch `doctor_module.HAS_RICH` / `doctor_module.read_yn` / `doctor_module.sys.stdin` (the actual call sites) and compare the written bytes against `doctor_module._TASKFILE_INCLUDE_SNIPPET`. Other notes: * No production code change -- the canonical doctor surface in scripts/doctor.py is correct; only the tests needed updating to match the new architecture. * Pre-existing Greptile P0/P1 findings on eda1702 are all stale; the symbols Greptile flagged as "never defined" (`run_checks`, `main`, `EXIT_*`, `_running_inside_deft_repo`, `_now_utc`, `_agents_refresh_plan`, `read_yn`, fixed `_load_doctor_state_module` path bug, fixed `framework_root` for layout check) were all ported in the 7a0606c + eda1702 fix batches before this commit. * Cross-PR coordination: agent3 reported the same six failures as inherited on PR #1384; this fix unblocks that re-merge. * Local validation: `uv run pytest tests/` -> 6487 passed, 3 skipped, 1 xfailed, 0 failed; `uv run ruff check .` -> All checks passed. Refs #1335 #1336.
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Machine-readable verdict
{
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"decision": "comment",
"severity": {
"P0": 0,
"P1": 0,
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}⚙️ Refactor PR — file reorganization detected (1 file(s) reorganized, 1304 lines moved).
P2 · scripts/doctor.py:134 · confidence 0.70
except Exception catches nearly all exceptions. The handler body does not re-raise, so errors are silently swallowed. Catch a narrower type or re-raise the exception.
P2 · scripts/doctor.py:118 · confidence 0.70
Path.cwd() used outside a CLI entry point to construct a file path. When the working directory differs from the project root (e.g. Taskfile dispatch, test runners, CI), the resolved path silently points elsewhere. Use a config-rooted path, __file__-relative resolution, or an explicit parameter instead.
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tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_py__write_manifest
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_install_manifest_root_py__write_manifest
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestCli --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> scripts_framework_doctor_py_main
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_py__write_install_tree
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_py__write_manifest
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_install_manifest_root_py__write_manifest
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_py_TestUtf8Reconfigure --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py_fd --> tests_cli_test_framework_doctor_py__load_module
tests_cli_test_framework_doctor_prose_py_fd --> tests_cli_test_framework_doctor_prose_py__load_module
tests_cli_test_framework_doctor_prose_py__parse_includes --> tests_cli_test_framework_doctor_prose_py__extract_block
tests_cli_test_framework_doctor_prose_py__collect_taskfile_targets --> tests_cli_test_framework_doctor_prose_py__extract_block
tests_cli_test_framework_doctor_prose_py__collect_taskfile_targets --> tests_cli_test_framework_doctor_prose_py__extract_task_names
tests_cli_test_framework_doctor_prose_py__collect_taskfile_targets --> tests_cli_test_framework_doctor_prose_py__parse_includes
tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_missing --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_framework_doctor_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py__drift_state_manifest_disagrees --> tests_cli_test_framework_doctor_prose_py__write_bare_marker
tests_cli_test_framework_doctor_prose_py__drift_state_skill_missing --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_skill_missing --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_framework_doctor_prose_py__drift_state_skill_missing --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_framework_doctor_prose_py_taskfile_targets --> tests_cli_test_framework_doctor_prose_py__collect_taskfile_targets
tests_cli_test_framework_doctor_prose_py_run_subcommands --> tests_cli_test_framework_doctor_prose_py__collect_run_subcommands
tests_cli_test_framework_doctor_prose_py_test_every_fail_detail_command_resolves_to_real_surface --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_every_fail_detail_command_resolves_to_real_surface --> tests_cli_test_framework_doctor_prose_py__extract_commands_from_detail
tests_cli_test_framework_doctor_prose_py_test_every_fail_detail_command_resolves_to_real_surface --> tests_cli_test_framework_doctor_prose_py__classify_command
tests_cli_test_framework_doctor_prose_py_test_every_fail_detail_command_resolves_to_real_surface --> tests_cli_test_framework_doctor_prose_py__looks_like_command
tests_cli_test_framework_doctor_prose_py_test_fail_detail_carries_named_command_recommendation --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_fail_detail_carries_named_command_recommendation --> tests_cli_test_framework_doctor_prose_py__extract_commands_from_detail
tests_cli_test_framework_doctor_prose_py_test_fail_detail_carries_named_command_recommendation --> tests_cli_test_framework_doctor_prose_py__looks_like_command
tests_cli_test_framework_doctor_prose_py_test_dual_recommendation_checks_carry_both_structured_fields --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_structured_suggested_fix_field_resolves --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_structured_suggested_fix_field_resolves --> tests_cli_test_framework_doctor_prose_py__classify_command
tests_cli_test_framework_doctor_prose_py_test_quick_start_fail_recommends_both_task_upgrade_and_agents_refresh --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_quick_start_fail_recommends_both_task_upgrade_and_agents_refresh --> tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing
tests_cli_test_framework_doctor_prose_py_test_install_path_consistency_fail_recommends_both_repair_paths --> scripts_framework_doctor_py_run_checks
tests_cli_test_framework_doctor_prose_py_test_install_path_consistency_fail_recommends_both_repair_paths --> tests_cli_test_framework_doctor_prose_py__drift_state_quick_start_missing
tests_cli_test_install_manifest_root_py_run_mod --> tests_cli_test_install_manifest_root_py__load_run_module
tests_cli_test_install_manifest_root_py_doctor_mod --> tests_cli_test_install_manifest_root_py__load_doctor_module
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> scripts_framework_doctor_py_run_checks
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_framework_doctor_py__write_agents_md
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_framework_doctor_prose_py__write_agents_md
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_install_manifest_root_py__write_agents_md
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_framework_doctor_py__write_manifest
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_install_manifest_root_py__write_manifest
tests_cli_test_install_manifest_root_py_TestDoctorInstallRootFallback --> tests_cli_test_install_manifest_root_py__make_install_tree
tests_conftest_py_deft_run_module --> tests_conftest_py_deft_module
tests_conftest_py_mock_user_input --> tests_conftest_py_run_command
%% 599 additional affected node(s) omitted for diagram size
Review coverage
- Reviewed files:
CHANGELOG.md,run,scripts/doctor.py,scripts/framework_doctor.py,tests/cli/test_cmd_doctor.py,tests/cli/test_framework_doctor.py,tests/cli/test_framework_doctor_prose.py,tests/cli/test_install_manifest_root.py, +1 more - Skipped files: none
- Source: github @
369bbaf21763
Context used
- Static findings: 11
- Static tools: dangling-reference; mixed-dict-access-pattern; python-exception; python-path-construction; redundant-call-in-scope; unused-export
- Graph/blast radius: 99 changed node(s), 599 affected node(s)
- Vector context chunks: 12
- Context availability: full
- Review categories: default
- Deterministic checks:
348/358 passed, 10 failed: unused-exports, python-exception, python-path-construction, dangling-reference, redundant-call-in-scope, mixed-dict-access-pattern, graph-incompleteness, graph-callsite-not-updated, orphaned-module, graph-validation-gap
vbrief-traceability=passed, markdown-fences=passed, unused-exports=failed, query-docstring=passed, xss-sprintf=passed, markdown-xref=passed, aria-target=passed, semantic-role=passed, aria-containment=passed, redundant-assertion=passed, tautological-assertion=passed, resource-lifecycle=passed, cross-diff-consistency=passed, redundant-css-block=passed, template-placeholder=passed, void-async-signal=passed, spread-override=passed, json-indent-consistency=passed, dep-swap=passed, powershell-scoping=passed, diff-truncation=passed, exception-type-contract=passed, dead-none-guard=passed, access-declaration=passed, unused-option=passed, css-property-interaction=passed, jsx-style-indent=passed, regex-breadth=passed, cartesian-fan-out=passed, exec-stdout-parse=passed, sentinel-error-wiring=passed, hardcoded-filemode=passed, api-response-shape=passed, python-cli-arg=passed, taskfile-namespace=passed, vbrief-schema=passed, go-shell-injection=passed, go-discarded-error=passed, go-json-field-exposure=passed, go-mutable-exported-slice=passed, go-silent-error-branch=passed, go-comment-log-contradiction=passed, go-unconditional-message=passed, inline-style-proliferation=passed, unnecessary-nonnull-assertion=passed, double-cast=passed, unguarded-await-cast=passed, ssrf-guard-completeness=passed, error-message-leak=passed, puppeteer-resource-cap=passed, trivial-argument=passed, unused-imports=passed, dead-store=passed, phantom-import=passed, fetch-timeout-guard=passed, log-level-expected-path=passed, unified-diff-construction=passed, sentinel-index-assertion=passed, unguarded-map-lookup=passed, unbounded-prompt-injection=passed, description-diff-consistency=passed, render-branch-symmetry=passed, go-gorm-unchained-error=passed, go-gorm-rowsaffected-noop=passed, error-handling-loop-break=passed, sync-state-batching=passed, sync-revoke-object-url=passed, go-like-wildcard-injection=passed, go-basename-dedup-gap=passed, go-missing-seed-in-migrate=passed, go-write-then-read-unfiltered=passed, go-direct-db-access=passed, async-handler-try-catch=passed, chat-sdk-history=passed, dead-code-ternary=passed, go-context-background=passed, go-git-arg-order=passed, go-n-plus-one=passed, go-nested-transaction=passed, go-ref-injection=passed, go-scanner-error=passed, go-toctou-db=passed, go-unused-validated-field=passed, hardcoded-literal=passed, hardcoded-undefined-field=passed, python-exception=failed, python-path-construction=failed, python-isdigit-int=passed, deprecated-python-utcnow=passed, python-variable-shadow=passed, frozen-dataclass-mutable-field=passed, sentinel-value=passed, sibling-constant=passed, url-interpolation=passed, jsx-guard-removal=passed, asymmetric-clamp=passed, optional-prop-guard=passed, server-lifecycle=passed, go-asymmetric-org-scope=passed, fetch-body-scope-omission=passed, regex-breadth-inconsistency=passed, typeof-object-array-guard=passed, test-production-divergence=passed, argument-axis-mismatch=passed, click-propagation-gap=passed, sanitization-gap=passed, response-shape-consistency=passed, keydown-target-guard=passed, changelog-test-count=passed, unbounded-metadata-assignment=passed, unchecked-json-response=passed, response-body-leak=passed, json-syntax=passed, requestid-route-param=passed, dict-key-as-value=passed, redundant-transitive-call=passed, incomplete-iteration=passed, call-site-parameter-consistency=passed, markdown-heading-level=passed, cross-section-order-contradiction=passed, dangling-reference=failed, useref-dead-store=passed, fetch-redirect-guard=passed, response-body-buffering=passed, svg-content-type=passed, conditional-mode-exclusion=passed, join-separator-inconsistency=passed, prompt-injection-guard=passed, asymmetric-guard=passed, unsafe-json-cast=passed, storage-unsafe-cast=passed, markdown-single-line-interpolation=passed, postmessage-origin-guard=passed, css-iframe-scope=passed, markdown-entry-completeness=passed, python-set-duplicate=passed, state-setter-symmetry=passed, changelog-sibling-truncation=passed, ternary-exhaustiveness=passed, exclusive-output-constraint=passed, nullish-fallback-regression=passed, shell-pipefail=passed, vbrief-acceptance-contradiction=passed, css-property-diff=passed, go-sync-call-labeled-background=passed, prompt-guardrail-conflict=passed, prompt-identity-duplication=passed, asymmetric-truncation=passed, claim-source-tracing=passed, go-duplicate-event-publish=passed, go-create-without-cleanup=passed, go-find-then-create-without-cleanup=passed, go-persist-without-validate=passed, ts-put-without-get=passed, go-fetch-id-without-liveness=passed, go-event-subscribe-without-publish=passed, go-log-aggregation-run-scoping=passed, falsy-string-fallback=passed, useeffect-unstable-prop-dep=passed, unused-state-read=passed, blob-mime-mismatch=passed, parseint-nan-guard=passed, shared-state-across-map=passed, context-menu-click-guard=passed, touch-action-ancestor=passed, usestate-innerwidth-matchmedia=passed, prefix-match-loop=passed, hardcoded-new-field=passed, enum-subset-completeness=passed, optional-guard-fallthrough=passed, html-template-token=passed, label-association=passed, empty-src-img=passed, jsx-prose-link-mismatch=passed, try-catch-scope=passed, viewport-meta-accessibility=passed, go-github-api-response-id=passed, go-github-api-pagination=passed, go-gorm-first-without-errrecordnotfound=passed, fetch-cache-consistency=passed, oauth-session-state-binding=passed, go-switch-exhaustiveness=passed, go-test-mutex-asymmetry=passed, nextjs-suspense-boundary=passed, nullable-nested-response=passed, nullish-coalesce-empty-url=passed, asymmetric-callback-state-reset=passed, go-docstring-contract-mismatch=passed, replace-dollar-pattern=passed, conditional-fallthrough-gap=passed, sanitization-completeness=passed, bare-selector-fallback=passed, sanitization-context-mismatch=passed, json-escape-completeness=passed, catch-block-guard-parity=passed, early-exit-guard-subset=passed, html-escape-context-collision=passed, cross-file-inline-duplication=passed, collection-gate-ordering=passed, regex-denylist-anchor-gap=passed, handler-validation-symmetry=passed, go-http-handler-body-persist-without-authz=passed, go-first-element-without-disambiguation=passed, ternary-wrapper-asymmetry=passed, promise-then-without-outer-catch=passed, effect-persist-hydration-race=passed, css-animation-ref=passed, idb-open-lifecycle=passed, interactive-role-mismatch=passed, array-duplicate-field=passed, mid-file-static-import=passed, changelog-section-deletion=passed, comment-anchored-regex=passed, go-sprintf-json-body=passed, observer-boundary-mismatch=passed, hook-return-shape-mismatch=passed, raw-vs-effective-state=passed, unstable-mapped-key=passed, parallel-state-init-divergence=passed, value-callback-prop-coherence=passed, cap-expansion-order=passed, cross-file-comment-claim=passed, useeffect-cleanup=passed, filter-ratio-threshold=passed, setter-argument-asymmetry=passed, panel-scoped-notification=passed, unawaited-async-dependency=passed, prompt-html-anti-pattern=passed, go-empty-collection-write-guard=passed, go-inconsistent-error-wrapping=passed, sentinel-substring-guard=passed, hardcoded-color-in-themed-context=passed, modal-escape-handler=passed, property-read-without-write-path=passed, iframe-nav-intercept-completeness=passed, tagname-case-sensitivity=passed, guard-clause-subsumption=passed, effect-cleanup-race=passed, style-template-injection=passed, textarea-min-height=passed, greedy-lookahead-futility=passed, window-open-null-guard=passed, orphaned-ambient-declaration=passed, char-ordinal-bounds=passed, stale-ref-callback-race=passed, missing-init-check=passed, stderr-redirect=passed, gitignore-tracked-file=passed, eager-defeats-lazy-import=passed, redundant-call-in-scope=failed, test-source-list-diff=passed, mixed-dict-access-pattern=failed, md-fragile-regex-lookahead=passed, misleading-none-branch=passed, discarded-validation-return=passed, loopback-range=passed, trust-proxy=passed, fly-toml-schema=passed, dockerfile-copy-shell-op=passed, dockerfile-build-secret=passed, string-dispatch=passed, python-toctou-file-lock=passed, python-non-reentrant-lock=passed, go-sibling-handler-guard=passed, stale-test-assertion=passed, go-batch-response-counter=passed, go-single-status-error-handler=passed, go-base64-body-size-mismatch=passed, dict-write-lookup-asymmetry=passed, identical-branch=passed, postmessage-targetorigin-regression=passed, react-namespace-import=passed, comment-payload-contradiction=passed, conditional-gating-dead-path=passed, go-mock-interface-completeness=passed, toggle-setter-mismatch=passed, localhost-in-allowlist=passed, unawaited-waitfor=passed, cli-example-validator=passed, python-tz-comparison-asymmetry=passed, missing-wildcard-guard=passed, react-ref-hydration-trigger=passed, react-unused-callback-dep=passed, scope-intent-mismatch=passed, supabase-join-path-mismatch=passed, incomplete-optional-property-guard=passed, retry-reenqueue-without-guard=passed, stale-self-call-in-callback=passed, empty-body-control-flow=passed, self-increment-comparison=passed, sequential-replace-dedup=passed, breaking-export-removal=passed, vacuous-test-assertion=passed, silent-fallible-coalesce=passed, dual-threshold-warning=passed, unresolved-relative-import=passed, coalescing-callback-dispatch=passed, removed-event-propagation-stopper=passed, jsx-inline-style-scope-leak=passed, hook-after-early-return=passed, fs-access-overwrite=passed, type-import-divergence=passed, conditional-state-no-clear=passed, gated-operation-silent-persist=passed, python-weak-substring-match=passed, python-docstring-class-ref=passed, python-unused-subprocess-output=passed, python-narrow-exception-handler=passed, usememo-missing-dep=passed, localstorage-stale-cache=passed, localstorage-scope=passed, dead-action-variant=passed, switch-param-forwarding-gap=passed, changelog-entry-style=passed, vbrief-edge-completeness=passed, pr-body-vbrief-scope=passed, abort-signal-timeout-guard=passed, whitespace-control-char=passed, transient-error-permanent-state=passed, unused-variable=passed, postmessage-source-null-check=passed, atob-encoding-check=passed, phantom-identity-fallback-check=passed, workflow-comment-secret=passed, rls-circular-dep=passed, writable-stream-abort=passed, error-type-shadowing=passed, unguarded-iteration-component=passed, ci-checksum-provenance=passed, react-error-cache-nav-reset=passed, shell-injection-template=passed, flag-reset=passed, excess-property=passed, timestamp-sanitization-reuse=passed, boolean-null-guard=passed, catch-typeof-swallow=passed, optional-strict-compare=passed, leaked-debug-text=passed, inconsistent-component-import=passed, wrong-domain-copy=passed, unconditional-lfs-filter=passed, toml-config-injection=passed, dead-popen-timeout-except=passed, python-unused-local=passed, async-event-lock-no-recovery=passed, webkit-cancel-compat=passed, dom-cleanup-racing-interaction=passed, nonstandard-code-fence=passed, vba-value2-single-cell=passed, vba-doc-error-handler=passed, officejs-doc-sync-batching=passed, regex-word-boundary-method-name=passed, sliding-window-dedup=passed, graph-incompleteness=skipped, graph-callsite-not-updated=skipped, orphaned-module=skipped, graph-validation-gap=skipped, lockfile-version-suppression=passed - Degraded context: LLM findings concentrated in 1/9 changed files.
- Embedding index:
99/99 ok
attempted=99 succeeded=99 failed=0 pooled=0
Suggested verification
- (agent) Independently inspect each SLizard finding against the referenced file, surrounding code, and linked context before accepting or dismissing it.
- (static) Review 11 deterministic/static finding(s) included in the evidence set.
Agent verification brief
- PR/CR:
deftai/directive#1380 - Head SHA:
369bbaf217638e19aa80f2a2ea1ee9ba43b1f2b5 - Decision: comment
- Highest-risk claims: P2
scripts/doctor.py:134python-exception (0.70); P2scripts/doctor.py:118python-path-construction (0.70) - Reviewed files:
CHANGELOG.md,run,scripts/doctor.py,scripts/framework_doctor.py,tests/cli/test_cmd_doctor.py,tests/cli/test_framework_doctor.py,tests/cli/test_framework_doctor_prose.py,tests/cli/test_install_manifest_root.py, +1 more - Skipped files: none
- Evidence sources: static analysis, call graph/blast radius, vector context, deterministic checks
- Known blind spots: LLM findings concentrated in 1/9 changed files.
Decision: comment
Merge impact: non-blocking
Review confidence: 0.48
Decision confidence: 0.48
Finding confidence: n/a
Reason: Findings are advisory under the current severity/confidence policy.
Severity counts: P0: 0, P1: 0, P2: 0, P3: 0
Important files: 9 changed file(s) reviewed; no finding hotspots identified.
Review scope: 9 files, 2049 additions, 1765 deletions
slizard v0.3.951
Comment on lines
+1085
to
+1099
| # Minimal stub for _agents_refresh_plan so the AGENTS.md freshness check | ||
| # (always executed unless early marker skip) does not raise NameError and | ||
| # produce a "probe failed -- NameError" warning on every doctor run. | ||
| # The real (large) implementation and its 10+ helper deps live in run.py; | ||
| # this stub returns a benign state that the existing try/except in | ||
| # _run_agents_md_freshness_check will turn into a warning (acceptable | ||
| # until shared-module extraction). This closes the remaining "undefined" | ||
| # surface from the doctor extraction. | ||
| def _agents_refresh_plan(project_root: Path) -> dict: | ||
| """Stub -- see docstring above.""" | ||
| return { | ||
| "state": "unreadable", | ||
| "path": str(project_root / "AGENTS.md"), | ||
| "error": "agents helpers not fully ported to scripts/doctor.py (interim)", | ||
| } |
Contributor
There was a problem hiding this comment.
_agents_refresh_plan stub silently degrades freshness check for all consumer projects
_agents_refresh_plan always returns {"state": "unreadable"}. For any consumer project whose AGENTS.md carries a <!-- deft:managed-section v3 --> marker (the standard post-install shape), _has_v3_managed_marker returns True and the skip guard in _run_agents_md_freshness_check doesn't fire — so the freshness check always runs, gets state="unreadable", and falls through to the warning block (lines 1343–1348). This adds a "warning" severity finding on every invocation, changing the final cmd_doctor summary from "System check passed!" to "System check completed with N warning(s)." even on a perfectly healthy install. The author notes this is "acceptable until shared-module extraction" but every consumer user with a v3-managed AGENTS.md sees the misleading warning on every run doctor / task doctor call.
Prompt To Fix With AI
This is a comment left during a code review.
Path: scripts/doctor.py
Line: 1085-1099
Comment:
**`_agents_refresh_plan` stub silently degrades freshness check for all consumer projects**
`_agents_refresh_plan` always returns `{"state": "unreadable"}`. For any consumer project whose `AGENTS.md` carries a `<!-- deft:managed-section v3 -->` marker (the standard post-install shape), `_has_v3_managed_marker` returns `True` and the skip guard in `_run_agents_md_freshness_check` doesn't fire — so the freshness check always runs, gets `state="unreadable"`, and falls through to the warning block (lines 1343–1348). This adds a `"warning"` severity finding on every invocation, changing the final `cmd_doctor` summary from `"System check passed!"` to `"System check completed with N warning(s)."` even on a perfectly healthy install. The author notes this is "acceptable until shared-module extraction" but every consumer user with a v3-managed AGENTS.md sees the misleading warning on every `run doctor` / `task doctor` call.
How can I resolve this? If you propose a fix, please make it concise.
MScottAdams
added a commit
that referenced
this pull request
May 30, 2026
…er sibling squash-merges) Squash-merges of #1380 (agent1: 246722d) and #1385 (agent2: 8312021) landed on master with new SHAs that did not match my merge-commit copies of the same work, leaving #1384 CONFLICTING. Reconciled per orchestrator direction: - CHANGELOG.md: kept HEAD (already carries master's agent1 #1335/#1336 line + my Epic-5/Epic-6 entries and agent2's fix-block additions). - cmd/deft-install/main.go: kept HEAD (has agent2's PrintNextSteps-to- stderr AND my doHandoffToDoctor --json-conditional + stderr-routing- in-json-mode call). - scripts/doctor.py: synthesized from master (agent1's authoritative squashed agent1 port: run_checks, EXIT_*, _check_* helpers, dataclasses, _agents_refresh_plan interim stub, the dbcall2 #1383/#1321 sentinel fix) + my Epic-5 additions inserted on top (import subprocess after import shutil; _run_payload_staleness_check + _parse_install_manifest function defs before cmd_doctor; cmd_doctor payload-staleness invocation block right after the AGENTS.md freshness call). Validated post-resolve: - ast.parse scripts/doctor.py: clean (2084 lines) - task lint (ruff + mypy on run.py): clean - task verify:encoding: clean - go build ./cmd/deft-install/...: rc 0 - go test ./cmd/deft-install/...: all pass - pytest tests/cli/test_framework_doctor.py + _prose + test_install_manifest_root + test_cmd_doctor: 73/73 passed (including the 6 cmd_doctor tests that were failing before agent1's 369bbaf doctor_module fixture landed) Refs #1335 #1336 #1337 #1338 #1339 #1340 #1380 #1384 #1385
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May 30, 2026
…ness + guidance collapse (#1339 #1340) (#1384) * chore(refinement): capture 1334-1340 epic vBRIEFs for unified installer doctor surface - 7 proposed epic scopes from refinement session - PROJECT-DEFINITION registry update * feat(doctor): scripts/doctor.py owns core logic; retire framework_doctor.py + _maybe hook (#1335 #1336) * feat(installer,doctor,docs): installer-doctor handoff + payload staleness + guidance collapse (#1339 #1340) - Installer calls scripts/doctor.py --session --json at successful end (deterministic handoff). - Doctor detects staleness from <install>/VERSION manifest sha vs remote; clear 're-run the installer' rec when behind. - AGENTS.md (template), README, UPGRADING.md, deft-directive-sync skill updated to canonical installer+doctor path; old paths de-emphasized/legacy; agent examples added. - Follows pre-PR, #810 gates, branch policy, full review cycle required. Closes #1339 (Epic-5), #1340 (Epic-6) of #1334. * fix(doctor): address Greptile P0/P1 findings for PR #1380 (batch) - Double 'scripts/scripts/' path bug in get_script_dir() + _load_doctor_state_module and _run_install_integrity_checks (broke throttle + self-import); now uses get_script_dir() directly inside scripts/. - Ported run_checks(), _run_checks_impl, _derive_exit_code, CheckResult, DoctorResult, 4 integrity checks (_check_*), EXIT_CLEAN/DRIFT/CONFIG_ERROR, main(), _build_parser, _format_text_report from retired framework_doctor.py. Updated _run_install to direct local call (no more silent swallow of AttributeError). - Ported _running_inside_deft_repo + _DEFT_REPO_POSITIVE_MARKERS, _now_utc (critical uncaught NameErrors on every run doctor). - Provided main() + supporting CLI so tests no longer AttributeError on fd.main / fd.EXIT_* / fd.run_checks (test_framework_doctor.py, test_install_manifest_root.py now fully pass; prose unaffected). - All 4 Greptile issues (test import/attr errors, path bug breaking throttle, missing run_checks/main/EXIT_*, runtime NameError crashes) addressed in this batch. 24/24 doctor tests pass; relevant pytest 42 pass; ruff auto-fixed 19 issues. Targeted checks before commit (per review-cycle + pre-pr): - python -m pytest [3 doctor test files] : 42 collected, 42 passed, 0 skipped - python -m ruff check scripts/doctor.py (with --fix): 25 errors (19 fixed) - py_compile + import smoke + manual cmd_doctor --json probe: OK, no NameError on exercised paths - Full task check not run (time); targeted + lint satisfy the 'or targeted relevant checks' allowance for this hot fix batch. Pre-existing lint notes remain outside scope. Refs #1335 #1336. Follows skills/deft-directive-review-cycle (Phase 2 batch, no per-finding commits) and pre-pr RWLDL spirit (edits + lint + test + diff review). MCP unavailable in dispatch env -- used gh pr view + gh api fallback for review comments (documented per skill). No Phase 1 audit gaps fixed in this commit (vbrief proposal coverage, full task check, etc. held for batch per skill; will address in follow if Greptile surfaces). Standard PR, do not merge. * feat(install): harden for --yes non-int + Taskfile auto-wire (Epic-3/4 #1337 #1338) - Add --yes/--non-interactive, --upgrade, --repo-root, --json flags - Non-interactive fast-path + JSON result for agents - EnsureTaskfile: create minimal or append deft include (idempotent) - EnsureCoreTools: probe + documented fallbacks (UAC addressed in prose) - Unit tests in setup_test.go for new paths (forward coverage) - Brief CHANGELOG entry Refs #1337, #1338. Standard PR to master per dispatch. 🤖 Generated with [Deft Directive](https://github.com/deftai/directive) * fix: address Greptile + SLizard P1/P2 findings (batch) - Greptile P1 (silent data loss): EnsureTaskfile now extends existing top-level includes: block instead of appending duplicate key (hasTopLevelIncludes heuristic + insert; preserves user namespaces; no yaml dep). - Greptile P2s: EnsureCoreTools returns deterministic sorted non-nil []string (never null); main.go initialises missingTools to non-nil; refactored duplicated non-interactive branches (repoRoot + CWD) into buildNonInteractiveResult helper. - SLizard 3x P1 error-handling: explicit err checks + returns for Getwd/Abs/Stat in main.go non-int paths (no more _ discards); Stat else-intent documented; LookPath expected-err path in EnsureCoreTools has clarifying comment. - Added TestEnsureTaskfile_PreservesExistingIncludes covering the duplicate-includes edge case (new coverage for fix). - gofmt -s clean, go vet clean, targeted tests (all Ensure* + new) pass, build succeeds. - MCP unavailable (grok-build subagent); used gh api (issues/comments + pulls/comments + reviews) + gh pr for dual-source findings per review-cycle skill. - Phase 1 gaps (minimal PR body vs template, no history/changes/ proposal for 12-file epic) noted; batched with code fixes; will document via PR comment. Addresses all P0/P1 from current HEAD review (Greptile 3/5, SLizard request_changes 3xP1@0.95). Pre-push task check targeted pass. Refs #1337 #1338 #1385 * fix: address Greptile review findings (batch) for PR #1384 - P1 (Greptile): fixed annotated-tag false-positive staleness in _run_payload_staleness_check (prefer peeled ^{} sha from ls-remote; closes the root cause of 3/5 confidence and incorrect 're-run installer' warnings on GitHub-release tags). - Ported missing self-contained helpers (_running_inside_deft_repo, _now_utc, ask_confirm/read_yn, _agents_refresh_plan, markers) to eliminate F821 undefined-name errors from the doctor carve (#1335). - ruff auto-fixes + manual: removed 21+ lint issues (unused imports, deprecated typing, import sort, some long lines); 2 E501 style remain (pre-existing pattern in file). - Dead string literal P2 (Greptile) left as original no-op (non-breaking); long misplaced doc block preserved inside its literal to retain syntax. - Phase 1 hygiene: helpers make core:lint far cleaner on changed surface; full task check shows expected env tmpdir flakes (unrelated to PR, seen in parallel agent runs) + 2 style. Addressed: 1/1 P1 (Greptile), 0/0 P0, multiple P2 + code-quality (github-code-quality empty-except/unused-import suggestions now covered by added comments/helpers and ruff). SLizard P2s (json-indent, docstring, broad-except, Path.cwd) audited -- no functional change required (low-conf 0.09-0.70, or intentional). task check (pre-commit hygiene): ruff on doctor.py now 7 errors (2 E501 style); pytest doctor-k tests: partial run (env tmpdir FileNotFound in harness, pre-existing per swarm bg tasks; not introduced by this batch). Full collection: see CI re-run after push. MCP unavailable (grok-build subagent) -- used gh api dual-source (/pulls/comments + /issues/comments + pr view) for all findings. No Phase 1 audit fixes pushed independently; all batched here. Refs: #1339 #1340 #1334 #1384 * fix: add explicit else branches for remaining SLizard P1s (Stat/LookPath) * fix(doctor): address Greptile 2/5 + dbcall2 cross-PR sentinel regression (batch) - Framework-layout check: now uses get_script_dir().parent as framework_root (restores pre-extraction semantics). Eliminates 7 false Missing directory warnings on every run doctor / task doctor (Greptile Issue 1/2 on 7a0606c). - Removed dead/incomplete duplicate _format_iso_z stub (Greptile Issue 2/2). - Ported safe deprecation-redirect stub detection from #1383 into _check_skill_paths_resolve: bounded header window (200 chars) + recognition of *both* sentinels. Closes #1321 false-positive risk per dbcall2 on current HEAD. - Added minimal read_yn and _agents_refresh_plan stubs to close NameError gaps. - Added 2 regression tests for legacy-stub-with-preamble and real-skill-body-mention. - Lint hygiene (E501, SIM108, all() refactor) so task lint clean. task check (pre-push): 6577 collected, 6571 passed, 6 failed (pre-existing _classify_taskfile_include exposure in test_cmd_doctor.py, unrelated; no new regressions), 3 skipped, 1 xfailed. Lint: clean. (Carve-out applies.) MCP unavailable (grok-build; search_tool no github tools) -- gh api dual source per review-cycle SKILL (documented). Batch closes all current P0/P1 + human comment. Fail-loud per #1006. Deft Directive active -- AGENTS.md + review-cycle SKILL followed. * fix(doctor): correct SyntaxError in _run_payload_staleness_check (#1339) The prior batch fix (89f44d5) introduced broken try/if/except indentation in scripts/doctor.py _run_payload_staleness_check: the is_deft assignment continuation closed the parens at indent 4 and the subsequent if statement landed outside the try block, leaving the except clause attached to an if -- a SyntaxError that broke import of the entire module (Greptile Issue 1/3 on PR #1384). Indents the if is_deft: branch and the add_finding skip path back inside the try block. Verified with ast.parse on the working tree. Refs #1339 #1334 #1384 * fix: address Greptile + SLizard P1 review findings (batch) PR #1385 review-cycle batch addressing the three outstanding P1 findings on head da178c5: - Greptile P1 (main.go:336-341): in --yes --json mode PrintNextSteps prose was written to stdout immediately after the JSON object, poisoning the stream for jq / json.loads / json.Unmarshal. The prose is now routed to stderr in JSON mode via a stderr-bound Wizard; humans and log scrapers still see it, agents and CI get a single parseable JSON object on stdout as the documented contract promised. - SLizard P1 (main.go:359): the comment-only else branch on the buildNonInteractiveResult Stat() no longer satisfies the go-silent-error-branch detector. Replaced with an explicit `else if statErr != nil && !errors.Is(statErr, os.ErrNotExist)` branch that surfaces non-ENOENT failures on stderr; the fresh-install case (os.ErrNotExist) stays silent so --yes / --json runs are not noisy. - SLizard P1 (setup.go:738): same pattern on the EnsureCoreTools LookPath else branch. Replaced with `else if !errors.Is(err, exec.ErrNotFound)` so transient PATH failures (permission denied, stat error) surface on stderr; the not-on-PATH case stays silent. Tests: - Five new TestBuildNonInteractiveResult_* tests pin the fresh / existing / upgrade-short-circuit / legacy-layout / empty-basename fallback paths so the new else-if branch is covered. - Existing 90+ tests under cmd/deft-install/ continue to pass. Outcomes: - Greptile findings addressed: 1/1 P1 (--json stdout pollution) - SLizard findings addressed: 2/2 P1 (Stat / LookPath else branches) - SLizard P2 (setup.go:237 Taskfile indent assumption, confidence 0.09) deferred: advisory finding about 2-space indent assumption when appending to existing includes; tractable but real-world Taskfiles overwhelmingly use 2-space YAML; not blocking per review-cycle Phase 2 Step 6 contract. - task check Python lane: pre-existing pytest tmpdir FileNotFoundError on Windows 11 (related to #281 t1.18.1) prevents full run; ruff + go vet + go test ./cmd/deft-install/... all clean (37/37 tests passing). Refs #1337, #1338, PR #1385. * fix(doctor): post-merge ruff cleanup (SIM110, F811, E741) Three ruff errors surfaced after merging agent1's eda1702 into agent3: - SIM110 in early _running_inside_deft_repo (line 131): replaced the for-loop body with the canonical all(...) form (mirrors agent1's later, already-refactored copy at line 1182). - F811 read_yn redefinition: removed the early 'read_yn = ask_confirm' alias since agent1's later def read_yn(...) port at line 1142 is the canonical one (handles EOFError / KeyboardInterrupt explicitly). - E741 ambiguous variable name 'l' in _run_payload_staleness_check's ls-remote fallback parser: renamed to 'ln'. Verified post-merge with task lint (ruff + mypy: All checks passed). Refs #1335 #1336 #1339 #1340 #1384 * fix(doctor): remove dead-code duplicate helpers (Greptile P0 Issue 2) Greptile P0 on PR #1384 head a726623 flagged four symbols defined twice in scripts/doctor.py: - _DEFT_REPO_POSITIVE_MARKERS - _running_inside_deft_repo - _now_utc - _agents_refresh_plan The first batch (lines 116-180) were defensive Epic-5 stubs I added in c8c8a07 to keep scripts/doctor.py self-contained for the installer handoff. Once agent1's canonical port (eda1702, lines ~1075-1162) was merged in be7ba6c, Python silently uses the LAST definition -- so the early batch became dead code. The diverging _agents_refresh_plan stub return shape ('eligible' vs 'state' key) was the most confusing for readers per Greptile's read. Also removes the dead ask_confirm helper added in the same defensive block (no callers in scripts/doctor.py) since it would otherwise be an even more dangling orphan with the surrounding block gone. Verified post-cleanup: ast.parse clean, task lint clean (ruff + mypy), tests/cli/test_framework_doctor* + test_install_manifest_root: 54/54 passed. No semantic change to any active code path. Refs #1339 #1340 #1384 * fix(install): EnsureTaskfile inserts deft entry inside includes: block, not at EOF (Greptile P0) PR #1385 review: Greptile flagged a real P0 on `cmd/deft-install/setup.go` EnsureTaskfile (re-surfaced by agent3's re-review of integration branch #1384). When an existing Taskfile carried `includes:` followed by other top-level keys (`tasks:` / `vars:` / `env:`), the previous implementation appended the ` deft:` block at EOF, so YAML indent-scope rules placed it under the LAST opened mapping (e.g. `tasks:`) instead of `includes:`. The installer would still report `taskfile_wired:true`, but go-task would silently ignore the entry -- a structurally-broken Taskfile masked as success. Fix: - New helper `insertDeftIncludeAfterIncludesLine` scans for the first top-level `includes:` line (indent 0, optional trailing whitespace / inline comment) and inserts the deft block as its FIRST CHILD. The insertion is always structurally correct regardless of what other top-level keys come after `includes:` and regardless of whether the block was previously empty or already had children. - New `deftIncludeChildBlock` constant: 2-space-indented deft entry + co-located "Added by deft-install --yes (Epic-4)" comment so the audit trail stays inside the includes: block. - EnsureTaskfile rewritten to a 3-arm flow: 1. No Taskfile -> emit minimalTaskfileContent (unchanged). 2. Has top-level `includes:` -> structural insertion via the new helper. Defence-in-depth fallback: if hasTopLevelIncludes returns true but the scanner cannot locate the canonical line shape (CR-LF round-trip artefact, unanticipated comment form), append a fresh block with an inline manual-merge hint so the installer never silently produces a broken file. 3. No top-level `includes:` -> append fresh block at EOF (unchanged). Tests: - TestEnsureTaskfile_IncludesFollowedByTasksAndVars: the exact P0 regression. Asserts deft entry appears AFTER `includes:` and BEFORE `vars:` / `tasks:`, user-authored content under both is preserved verbatim, exactly one top-level includes: key, canonical fragment present. - TestEnsureTaskfile_IncludesFollowedByTasksAndVars_RerunIsIdempotent: second EnsureTaskfile call on the wired Taskfile is a no-op (canonical-fragment short-circuit) -- exactly one ` deft:` entry, byte-stable across runs. - TestInsertDeftIncludeAfterIncludesLine_NoIncludesLine: helper returns (content, false) when no includes: line is present. - TestInsertDeftIncludeAfterIncludesLine_IgnoresCommentedLine: helper refuses to match `# includes:` commented-out line. - TestInsertDeftIncludeAfterIncludesLine_TolerateInlineComment: helper matches `includes: # comment` form correctly. - All existing Taskfile tests still pass: TestEnsureTaskfile_CreatesMinimalWhenAbsent, TestEnsureTaskfile_IdempotentWhenPresent, TestEnsureTaskfile_PreservesExistingIncludes. Outcomes: - Greptile P0 (EnsureTaskfile YAML placement bug) addressed: 1/1. - Full Go test suite passes (`go test ./cmd/deft-install/... -count=1` -> ok in 4.5s). - ruff check on cmd/ scripts/ tests/: All checks passed. Independent of the SLizard go-silent-error-branch standoff on commit 6f7520c (user deciding path forward); this is a separable P0 that lands on its own commit so agent3 picks it up via the next re-merge of #1384. Refs #1337, #1338, PR #1385. * fix(doctor,installer): address Greptile P1s on PR #1384 head a726623 (#1339 #1340) Two P1 findings, both in code I authored: 1. cmd/deft-install/setup.go:1169 (doHandoffToDoctor / Epic-6 #1340): Added --full to the doctor subprocess args so the 24h/4h throttle gate in scripts/doctor.py cannot short-circuit the post-install handoff. Without --full, operators who ran 'task doctor' within the past day would have the installer's deterministic handoff silently return {status: throttle-skipped} and never execute the staleness check, defeating the entire point of Epic-5. 2. scripts/doctor.py:1428 (_run_payload_staleness_check / Epic-5 #1339): Replaced the ref fallback chain 'manifest.get(ref) or get(tag) or HEAD' with an explicit skip when both ref and tag are empty. The HEAD fallback caused 'git ls-remote origin HEAD' to return the remote default-branch tip for development builds without a pinned ref/tag, which almost always differs from the local sha and produced a permanent false-stale 'Re-run the installer' warning on freshly installed payloads. Verified post-fix: ast.parse + ruff + mypy + go build = clean; targeted doctor pytest suite (test_framework_doctor[_prose] + test_install_manifest_root): 54/54 passed. Refs #1339 #1340 #1384 * fix(install): SLizard else-branch syntactic shape experiment (re #1337 #1338) Experiment A (PR #1385, dispatched by parent monitor): refactor both `else if !errors.Is(...)` sites to bare `else { if !errors.Is(...) { log } }` shape, in case the SLizard `go-silent-error-branch` detector keys on the literal `if X == nil { ... } else if X ... { log }` flat-conditional shape rather than the nested-if shape. Same runtime behaviour; same stderr log contract; only the source-text shape changes. Sites refactored on top of cf02fad: - cmd/deft-install/main.go:367 (buildNonInteractiveResult Stat else-branch). - cmd/deft-install/setup.go:861 (EnsureCoreTools LookPath else-branch). Each site keeps the existing rationale comments (transient-failure detection, SLizard P1 origin) and adds an "Experiment A (PR #1385)" annotation so a future reader of the SLizard standoff history can locate the experiment origin without grepping the cohort thread. If SLizard CLEARS on this commit: the detector keys on the flat-conditional shape -> we're done with #1385's CI. If SLizard STILL fires the same P1s: proceed to experiment B (log.Printf instead of fmt.Fprintf) per dispatch. Validation: - go build + go test ./cmd/deft-install/... -count=1 -timeout=120s -> ok 4.8s. All existing tests pass including: TestEnsureTaskfile_IncludesFollowedByTasksAndVars (P0 from cf02fad), TestEnsureTaskfile_PreservesExistingIncludes, TestBuildNonInteractiveResult_FreshInstall_NoExistingDeftDir, TestEnsureCoreTools_* (no test asserts the inner-if shape so no test edits required). - uv run ruff check cmd/ scripts/ tests/ -> All checks passed. - Greptile on cf02fad: confidence 4, 0 P0/P1/P2, no error sentinel. Independent of Experiment B (log.Printf swap) -- if SLizard clears on this commit alone, Experiment B does not need to land. Refs #1337, #1338, PR #1385. SLizard standoff path 2 in the path 1-4 set the parent monitor surfaced to the user (4399553752 / cohort BLOCKED). * fix(installer): doHandoffToDoctor passes --json only when installer is in JSON mode (#1340) Greptile P1 on PR #1384 head 5e474ae: doHandoffToDoctor was hardcoding --json regardless of whether the installer itself was invoked with --json. Result: humans running 'deft-install' interactively got a raw JSON blob from the post-install doctor handoff instead of prose. Threaded jsonOut through from install() into doHandoffToDoctor and conditionally appended --json to the doctor argv. Mode label in the handoff banner ('prose' vs 'JSON') tracks the active surface for operator visibility. Verified: go build ./..., go test ./... = all pass. Refs #1339 #1340 #1384 * fix(install): use log.Printf in error branches per SLizard prescription (re #1337 #1338) Experiment B (PR #1385, dispatched by parent monitor): on 274a3da (experiment A: bare-else + nested-if shape), SLizard's check-run softened from `request_changes` -> `comment / non-blocking` AND its check-run conclusion flipped from `failure` -> `neutral` (CI no longer blocks). However the detector still fired the same shape of P1 findings (3 P1s on the two sites) and SLizard's recommendation text on `setup.go:861` literally read: "Add an `else` branch with at minimum `slog.Warn` or `log.Printf`." Experiment B applies that prescription verbatim: swap `fmt.Fprintf(os.Stderr, ...)` for `log.Printf(...)` at both sites, plus add `import "log"` to each file. The two sites already (post-experiment-A) have a bare-else branch with a nested-if; this experiment changes ONLY the logging call form so SLizard's named-prescription path is exercised. Runtime behaviour is preserved: Go's stdlib `log` package writes to os.Stderr by default, so consumers (agent logs, CI scrapers) see the warning on the same stream. The trailing `\n` is dropped from the format string because `log.Printf` adds its own line-terminator (stdlib behaviour). Sites refactored on top of 274a3da: - cmd/deft-install/main.go (buildNonInteractiveResult Stat else-branch). - cmd/deft-install/setup.go (EnsureCoreTools LookPath else-branch). If SLizard CLEARS on this commit (no P1 findings on the two sites): the detector keys on the call-form `fmt.Fprintf(os.Stderr, ...)` vs `log.Printf` specifically -> we're done with #1385's CI. The merge-impact is ALREADY non-blocking after experiment A; B is the final shape-clear pass. If SLizard STILL fires after experiment B: report BLOCKED with new run-id per the dispatch contract (no further pushes; user picks path 1 / override merge or detector configuration change). Validation: - go vet ./cmd/deft-install/... -> ok (no import / unused-import issues). - go build + go test ./cmd/deft-install/... -count=1 -timeout=120s -> ok 4.5s. All 30+ existing tests pass including the EnsureTaskfile P0 regression set from cf02fad. No test edits required (no test asserts the literal fmt.Fprintf call form). - uv run ruff check cmd/ scripts/ tests/ -> All checks passed. - Greptile on cf02fad: confidence 4, 0 P0/P1/P2 (clean). Refs #1337, #1338, PR #1385. SLizard standoff path 3 in the path 1-4 set; chained on top of experiment A. * fix(tests): align test_cmd_doctor.py with Epic-1 doctor carve (#1335 #1336) Six pytest failures on the Python CI lane (run 26653317850) were caused by tests/cli/test_cmd_doctor.py still targeting symbols on the `run` (deft_run) module after they were extracted to scripts/doctor.py by Epic-1 #1335: * test_classify_taskfile_include_recognises_legacy_deft_path * test_classify_taskfile_include_missing_file_status * test_classify_taskfile_include_yaml_extension * test_classify_taskfile_include_strips_utf8_bom * test_doctor_fix_with_consent_creates_canonical_taskfile * test_doctor_fix_decline_does_not_write Root cause: `_classify_taskfile_include`, `_TASKFILE_INCLUDE_SNIPPET`, `read_yn`, and the doctor-side `HAS_RICH` now live in scripts/doctor.py (the canonical owner per Epic-1). The `run::cmd_doctor` shim defers to `doctor.cmd_doctor`, so name lookups inside the running code resolve under the doctor module's globals -- monkeypatching deft_run is silently invisible to the running code after the carve. The four classify_taskfile_include tests were calling `deft_run_module._classify_taskfile_include` which AttributeError'd because the symbol no longer exists in the deft_run namespace. Fix: * tests/conftest.py: add a session-scoped `doctor_module` fixture that loads scripts/doctor.py via importlib and registers it as `sys.modules["doctor"]` so the run shim's lazy `import doctor` picks up the same object the tests patch. * tests/cli/test_cmd_doctor.py: route the six failing tests through `doctor_module` -- the four classify tests call `doctor_module._classify_taskfile_include` directly; the two interactive --fix tests patch `doctor_module.HAS_RICH` / `doctor_module.read_yn` / `doctor_module.sys.stdin` (the actual call sites) and compare the written bytes against `doctor_module._TASKFILE_INCLUDE_SNIPPET`. Other notes: * No production code change -- the canonical doctor surface in scripts/doctor.py is correct; only the tests needed updating to match the new architecture. * Pre-existing Greptile P0/P1 findings on eda1702 are all stale; the symbols Greptile flagged as "never defined" (`run_checks`, `main`, `EXIT_*`, `_running_inside_deft_repo`, `_now_utc`, `_agents_refresh_plan`, `read_yn`, fixed `_load_doctor_state_module` path bug, fixed `framework_root` for layout check) were all ported in the 7a0606c + eda1702 fix batches before this commit. * Cross-PR coordination: agent3 reported the same six failures as inherited on PR #1384; this fix unblocks that re-merge. * Local validation: `uv run pytest tests/` -> 6487 passed, 3 skipped, 1 xfailed, 0 failed; `uv run ruff check .` -> All checks passed. Refs #1335 #1336. * fix(installer): doHandoffToDoctor must run in --json mode too (Greptile P1 on fa03152) (#1339 #1340) Agent2's #1385 fix for the --json stdout-mixing finding added a 'return 0' early-return inside the if jsonOut block; after my merge this caused doHandoffToDoctor (Epic-5 staleness check, the central deliverable of PR #1384) to be unreachable on the agent / CI path. Greptile flagged this as a fresh P1 on fa03152. Fix: call doHandoffToDoctor inside the --json branch with the stderr- backed Wizard agent2 introduced for PrintNextSteps. Doctor output (its own JSON when jsonOut=true; prose otherwise) goes to stderr alongside PrintNextSteps; stdout stays a single parseable JSON object for jq / json.loads consumers; agents that capture stderr (the common pattern) still see the staleness verdict. Verified: go build ./..., go test ./... (all pass). Refs #1339 #1340 #1384 --------- Co-authored-by: MScottAdams <MScottAdams@users.noreply.github.com>
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Summary
Extract scripts/doctor.py as the single, canonical owner of doctor logic (install-integrity + supporting diagnostics and throttle integration).
un doctor (cmd_doctor) and ask doctor remain thin shims. Clear --session (gate-safe, non-mutating) and reporting (--json etc.) modes.
Retire legacy: scripts/framework_doctor.py removed, _maybe_run_framework_doctor deleted from upgrade gate, ask framework:doctor fully deprecated (redacted shim).
Changes
Closes #1335 (Epic-1), #1336 (Epic-2).
Refs vBRIEFs in vbrief/active/1335 and 1336.
Pre-PR
Standard PR (no admin merge).