Add unified repo graph, intent-native memory, and Pro/Team hardening#19
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Pre-PR Code Review — APPROVE-pending (sound; CI green)
Verdict: APPROVE (pending merge-gate). No security, logic, or quality blockers found. Code is well-structured, well-tested, and CI is fully green across all 7 checks.
What this PR does:
A major feature addition to Engraphis (5595 additions, 310 deletions across 60+ files):
- Schema v3 logical graph layers (temporal, entity, causal, semantic) with layered edges in the same SQLite store
- Incremental multi-language code indexing (adding Go, Rust, Java, SQL, Terraform support)
- Code↔memory linking, path queries, community/hotspot analysis, git/PR impact, portable graph exports (JSON/HTML/Markdown)
- Intent-native recall (
remember/link/recall) with durable link rationale - Privacy-safe SHA-256 receipt chains (content-free, tamper-evident)
- Optional LLM retention supervision (advisory only, never silently drops writes)
- Local resource ingestion (text/code/HTML/DOCX) + optional PostgreSQL catalog adapter
- Read-only graph server (
engraphis-graph-server) with bearer token auth - 7 new MCP tools (27 total): code_path, code_impact, export_code_graph, receipts, verify_receipts, export_receipts, ingest_postgres_schema
- Updated docs, architecture document, SECURITY.md hardening, skills, and tests
Security review:
- PostgreSQL DSN handling: DSN is used only for the connection, never stored, returned, logged, or embedded in memory (only a one-way digest in provenance). Confirmed in postgres_schema.py.
- Receipt chains: Content-free — raw memory text, workspace names, IDs, and actor identities are excluded from exported payloads. Confirmed in test_receipts.py.
- Retention supervision: Advisory only — the engine validates/clamps LLM results; writes are never silently discarded. Confirmed in retention.py.
- Resource ingestion: Path-traversal guards, size/count bounds,
trusted:falseon imported files. Missing optional tools fail actionably. - Read-only server: No mutation routes; non-loopback binding requires a bearer token. Documented in SECURITY.md.
- SQL injection: PostgreSQL introspection uses parameterized queries (
%splaceholders). Confirmed.
Quality review:
- CI: ALL GREEN (7 checks covering Python 3.9-3.12, lint, wheel build, docker smoke)
- Tests: 845 collected; new test files cover receipts (concurrent chains), postgres schema (valid + malicious), protocol upgrades, read-only API, resources, retention, graph CLI, packaging
- Eval: ablation harness shows hybrid PPR recall 1.0; multi-hop graph PPR 1.0
- Comprehensive docs: ARCHITECTURE_V3.md, updated AGENTS.md, README, KILO_CODE_INTEGRATION, SECURITY.md
ruff check .clean;python -m compileallclean
Minor notes (non-blocking):
- Single commit with no incremental review history on a 5595-addition PR — consider splitting future large features into smaller reviewable chunks
- PR is <6h old with a single cowork-bot author — cannot formally APPROVE per fleet merge-gate
Formal APPROVE withheld per fleet self-approval embargo + <6h/<3-contributor gate. This PR is approval-ready once the merge-gate conditions are satisfied.
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Release-readiness follow-up is complete on The reasonless automated REWORK verdict was treated as a prompt for a fresh adversarial audit rather than dismissed. The audit found and fixed concrete blockers in Team auth concurrency/token lifecycle, relay quota/streaming/redirect security, secret and personal-workspace sync isolation, receipt tail integrity, shared-folder and merge-driver hostile-input handling, PostgreSQL parameterization, and fresh Python 3.10 dependency resolution. Final state: current |
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💡 Codex Review
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Reviewed commit: 5d9c4e8458
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| CREATE TABLE IF NOT EXISTS code_files ( | ||
| repo_id TEXT NOT NULL, | ||
| file TEXT NOT NULL, | ||
| lang TEXT, | ||
| content_hash TEXT NOT NULL, | ||
| size_bytes INTEGER DEFAULT 0, | ||
| mtime_ns INTEGER DEFAULT 0, | ||
| backend TEXT DEFAULT '', | ||
| indexed_at REAL, | ||
| PRIMARY KEY(repo_id, file) | ||
| ); | ||
| CREATE INDEX IF NOT EXISTS idx_code_files_lang ON code_files(repo_id, lang); | ||
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| CREATE TABLE IF NOT EXISTS code_memory_links ( | ||
| id TEXT PRIMARY KEY, | ||
| repo_id TEXT NOT NULL, | ||
| symbol_id TEXT NOT NULL, | ||
| memory_id TEXT NOT NULL, | ||
| relation TEXT DEFAULT 'mentions', | ||
| confidence REAL DEFAULT 1.0, | ||
| created_at REAL, | ||
| UNIQUE(repo_id, symbol_id, memory_id, relation) |
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When MemoryService.copy_workspace() copies an indexed repository, it clones symbols and code edges but does not clone the new code_files rows or remap/copy code_memory_links. Consequently, a copied workspace immediately exports a graph with zero files and loses every memory↔symbol association, even though the corresponding symbols, memories, and repository were copied. Copy these records using the new repo, symbol, and memory ID mappings.
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| CREATE TABLE IF NOT EXISTS code_memory_links ( | ||
| id TEXT PRIMARY KEY, | ||
| repo_id TEXT NOT NULL, | ||
| symbol_id TEXT NOT NULL, | ||
| memory_id TEXT NOT NULL, | ||
| relation TEXT DEFAULT 'mentions', | ||
| confidence REAL DEFAULT 1.0, | ||
| created_at REAL, | ||
| UNIQUE(repo_id, symbol_id, memory_id, relation) | ||
| ); | ||
| CREATE INDEX IF NOT EXISTS idx_code_mem_symbol | ||
| ON code_memory_links(repo_id, symbol_id); | ||
| CREATE INDEX IF NOT EXISTS idx_code_mem_memory | ||
| ON code_memory_links(repo_id, memory_id); |
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When merge_workspaces() finds the same repo name in both workspaces, it moves symbols and code_edges to the surviving repo and deletes the source repo, but it never updates the new code_memory_links table. The source workspace's links are therefore left under a deleted repo ID and disappear from code search, graph export, and impact results after a merge; move or rebuild those links as part of the repo remap.
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Reviewed commit: 9b3274b3cb
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| for link in self.store.links_among( | ||
| [r.id for r in recs], layers=flt.graph_layers | ||
| ): |
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When graph_mode="1hop" is selected (and when PPR falls back to _graph_arm_1hop for a large graph), the new layer restriction is bypassed: _graph_arm_1hop calls store.neighbors(seed_ids, at=now), whose query has no layer predicate. Thus an intent such as timeline can traverse causal/entity edges despite its requested layers, producing graph-derived recall results outside the selected overlay. Thread flt.graph_layers through neighbors() and the 1-hop call as well.
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Pre-PR Code Review — VERDICT: APPROVE-pending (sound; formal approval withheld by gate)
SummaryLarge but well-structured feature PR: unified repo graph, intent-native memory, Pro/Team hardening. 82 files, +8,429 / −537. Analysis
Required before formal APPROVE
Notes
Verdict: APPROVE-pending — green, tested, no security findings. Withhold formal merge approval until gate #1–#2 clear. |
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Follow-up hardening for the unintentionally merged PR #19, from a fresh adversarial review plus the open Codex thread: - Thread graph_layers through Store.neighbors() so 1-hop graph recall (and the PPR large-graph fallback) honors the layer overlay (Codex P2) - FolderTransport.push(): unpredictable temp name + O_CREAT|O_EXCL|O_NOFOLLOW so hostile peers can't redirect our write through planted symlinks - engraphis-graph-server: empty --host/ENGRAPHIS_GRAPH_HOST binds all interfaces, so treat it as non-loopback and require the bearer token - Strip the reserved metadata.retention_supervision key from caller metadata at the service boundary (raw stability/importance bypass of the bounded retention_class presets) - merge_workspaces(): fold overlapping file snapshots without duplicating symbols/code edges; remap losing-side memory links by fqname - graph_cli: reject leading-dash git revisions (option injection), refuse a symlinked export directory, write exports atomically - service.graph(): bound entity edges and code edges/links via a limit-derived cap end-to-end (SQL LIMITs included) - Relay sync fails closed on unreadable workspace settings in both the CLI and dashboard/background paths; resources.extract_bytes enforces its own raw-size cap; importance clamp made consistent in _retention_signal; vendor package-data glob covers nested assets Offline gate green off-mount: 78/78 test files (912 tests incl. 10 new), sample+codemem evals 1.000, ablation unchanged, ruff and compileall clean.
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Summary
main(eaf8a1a) so the compact Settings/agent panel ships alongside the new graph, import, and receipt controlsRelease-readiness findings fixed
secretmemoriesonnxruntimeline only where Python 3.10 needs itUser and developer impact
Validation
python -m pytest tests/ -q: 896 tests collected; full suite greenruff check .,python -m compileall -q engraphis scripts tests, andgit diff --check1.0001.0; multi-hop graph PPR1.0versus one-hop0.0pip-audit: no known vulnerabilitiestwine checkpasses; wheel-content check passes with the intentional top-levelscriptspackage warnings allowed; clean wheel import passes5d9c4e8, including Docker health/readinessReview status
REWORKverdict predates both hardening passes and supplied no concrete reasonmainis integrated