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Umbrella design (signals-wiki-unification) plus six sequenced workstream specs: storage relocation (B), migrate framework (C), command/agent/skill unification (D), drift scope (E), agent model overrides (F), Cobra migration (A).
Storage path constants move from .claude/project/ to docs/wiki/: signalsFile -> docs/wiki/scan.md (no YAML frontmatter), prevFile -> tmp/.scan.prev.md. ScanWithOptions no longer emits frontmatter; idempotency and Stale compare raw body directly. LinkifyFiles points at the docs/wiki/ router (index.md) and flat domain files, excluding scan.md/CLAUDE.md/index.md. tree.go skips docs/wiki/scan.md so the dump does not appear in its own tree. Workstream B / CP1 of signals-wiki unification.
… ref Doctor signals/refs checks adapt to the relocated layout: router at docs/wiki/index.md, ref @docs/wiki/index.md, domain files flat under docs/wiki/ (orphan enumeration excludes index.md/scan.md/CLAUDE.md by basename). fix.go --fix wires @docs/wiki/index.md. Workstream B / CP2 of signals-wiki unification.
…rol blocks Relocate every storage path in the inferrer template to docs/wiki/: router docs/wiki/index.md (OKF type: Index + <wiki-type>repo</wiki-type>, <scan-sha> via git hash-object, <wiki-schema>1</wiki-schema>), flat domain files docs/wiki/<domain>.md (OKF type: Domain), scan docs/wiki/scan.md, prev tmp/.scan.prev.md, @-ref @docs/wiki/index.md. New Step 8c bootstraps docs/wiki/CLAUDE.md steering (idempotent, never clobbers). Wiki-output mode reads <tmp>/docs/wiki/scan.md. Agent name unchanged (signals). Bundle regenerated. Workstream B / CP3 of signals-wiki unification.
signals-gate stages docs/wiki/index.md + domains (excludes raw scan.md); refresh-signals relocates scan/router/@-ref paths and moves steering to docs/wiki/CLAUDE.md (OKF type: Steering, create-if-absent); refresh-wiki member-detection prose -> docs/wiki/index.md; cliusage scan/show/linkify descriptions name docs/wiki paths; golden test updated. Bundle + rendered commands regenerated. Workstream B / CP4 of signals-wiki unification.
frontmatterTypeToClass maps type: Index -> index and type: Domain -> domain; app.css adds --c-index/--c-domain palette vars (light+dark); layout.html registers index/domain in atomicCyTypeColors + typeNames so the dynamic legend and node coloring pick them up. docs/wiki/ signals docs now render as first-class typed nodes in atomic serve. Workstream B / CP5 of signals-wiki unification.
git mv .claude/project/signals.md -> docs/wiki/index.md and 9 domain files -> docs/wiki/<domain>.md; deterministic-signals.md -> docs/wiki/ scan.md (regenerated). Add OKF frontmatter (Index/Domain/Steering), index.md control blocks (<wiki-type>/<scan-sha>/<wiki-schema>), bootstrap docs/wiki/CLAUDE.md steering. Rewire @-ref to @docs/wiki/index.md, fix depth-3 -> depth-2 relative links, drop obsolete .gitignore prev path, exclude docs/wiki/ from the VitePress site. Doctor refs PASS. Workstream B / CP6a of signals-wiki unification.
README signals diagram, docs/reference/signals-workflow.md +
wiki-workflow.md, and the atomic-help detection probe + state-files tour
now name docs/wiki/{index,scan}.md and the docs/wiki/CLAUDE.md steering
file. Rendered atomic-help + bundle regenerated.
Workstream B / CP6b of signals-wiki unification.
docs/wiki/ is generated signals output (router, domains, scan, steering), not source. Including it made the scan self-referential: the <scan-sha> hash written into index.md changed index.md's blob SHA, changing the tree, so 'atomic signals stale' returned exit 1 forever. Skip the whole docs/wiki/ dir, mirroring the already-skipped .claude/project/. Workstream B / CP6c of signals-wiki unification.
Regenerate docs/wiki/scan.md against the final tree (docs/wiki/ now excluded) and stamp <scan-sha> to match. atomic signals stale is fresh.
parseRouterDomains used an inTable flag that flipped false on the first prose line after '## Domains' — but the router has an intro paragraph before the table, so zero domains parsed and every real domain file was falsely flagged as an orphan. Switch to section-based scanning: enter on '## Domains', exit on the next '## ' heading, parse only table rows in between. Workstream B / CP6d of signals-wiki unification.
parseRouterDomains read the Detail column as cols[4], but domain one-liners may contain unescaped pipes (the serve row: md|code, [page|system]), shifting the split. Detail is always the last content column and pipe-free, so read cols[len(cols)-2]. Workstream B / CP6e of signals-wiki unification.
Unifies per-repo signals storage under docs/wiki/ with OKF frontmatter and the <wiki-type>/<scan-sha>/<wiki-schema> control blocks — the foundation for the signals/wiki unification. - scan -> docs/wiki/scan.md (no frontmatter), prev -> tmp/.scan.prev.md - router -> docs/wiki/index.md (type: Index + control blocks), @-ref'd - domains -> flat docs/wiki/<domain>.md (type: Domain) - steering -> docs/wiki/CLAUDE.md (type: Steering) - doctor, inferrer, signals-gate, cliusage, serve graph relocated - this repo migrated; docs/wiki/ excluded from scan tree + VitePress site Agent name and /refresh-signals kept (workstream D renames).
New atomic/internal/migrate package: Migration{TargetVersion,Scope,Up}
type, ordered Registry, and Run() that applies steps with TargetVersion
semver-greater than the recorded version in ascending order, stop-on-
error, empty recorded treated as a 0.0.0 floor, caller slice not mutated.
Adds exported selfupdate.CompareSemver(a,b) as the canonical compare
(malformed inputs floored to 0.0.0) so migrate reuses semver parsing
instead of duplicating it.
Workstream C / C1 of signals-wiki unification.
Add the [install] TOML table: version (semver) + [install.artifacts] per-kind lists (agents/commands/skills/output-styles/rules). knownSchemaKeys accepts install.* without unknown-key warnings; install keys are machine- written (not surfaced in 'atomic config list'). checks_config validates install.version as semver via the reused selfupdate.IsValidSemver; a config with no [install] table is valid (pre-framework state). Workstream C / C2 of signals-wiki unification.
On a non-dry-run install: write [install].version + [install.artifacts] to config.toml (per-kind target lists), and prune artifacts present in the prior manifest but absent from the current bundle (pure PruneDiff + deny-by-default batched confirm seam; Ctrl+C/non-interactive = decline, never an install failure). Only install.artifacts entries are ever prune-eligible, so user-added files are untouchable. uninstall.go scopes removal to the manifest (nil = pre-framework fallback). Workstream C / C3 of signals-wiki unification.
… hook New 'atomic migrate' verb: no flags = install-scope (config [install]. version anchor); --repo reads/writes the <wiki-schema> block in the repo's docs/wiki/index.md; --realm runs install-scope then prompts per member repo (non-interactive/abort = skip, never auto-migrate). First registered step relocates .claude/project/signals* -> docs/wiki/ — resumable (completion sentinel <wiki-type> written last), idempotent (moveFile skips already-moved, refuses to clobber an existing target), atomic content writes. runUpdate runs install-scope migrations after the artifact refresh (warn-not-fatal). cliusage registers migrate (A1 clean). Workstream C / C4 of signals-wiki unification.
Doctor check 12 (migrate): when config [install].version is older than the running binary, WARN to run 'atomic migrate' (artifacts/migrations behind the binary); PASS when [install] is absent (pre-framework) or the binary is 'dev'. /atomic-help lists 'atomic migrate [--repo|--realm]' in the binary topic + maintenance tour; docs/guides/install.md gains a Migrations section (update auto-runs steps; migrate --repo/--realm). Workstream C / C5 of signals-wiki unification.
Versioned, replayable migration framework backed by install state in
config.toml [install].
- migrate package: Migration{TargetVersion,Scope,Up} + ordered Registry
+ semver-ordered Run (exported selfupdate.CompareSemver)
- config [install].version + [install.artifacts] schema v2
- install writes the manifest; prune removes dropped artifacts (data-safe
batched confirm); uninstall scopes to install.artifacts
- atomic migrate verb (--repo reads <wiki-schema>, --realm fans out with
per-repo confirm); first step relocates signals -> docs/wiki/ (resumable,
idempotent, refuses to clobber); atomic update auto-runs install-scope
migrations
- doctor check 12 nudges when binary newer than [install].version
Rename the inferrer agent (template + rendered) and update every dispatch site (signals-gate, autopilot, subagent-implementation, refresh-wiki, atomic-setup, atomic-help, CLAUDE.md). The agent's system prompt gains an imperative authoritative-steering clause: read docs/wiki/CLAUDE.md and treat it as authoritative before inferring. Stale embedded bundle copy pruned. Bundle regenerated. Workstream D (CP2+CP4) of signals-wiki unification.
/refresh-wiki is now the single refresh verb for both repo and realm
scope (Step 0 detects <wiki-type>). The atomic-wiki skill is a thin
router (95 lines); the full per-scope pipelines live in
skills/atomic-wiki/references/{repo,realm}.md. atomic-wiki-inferrer is
thinned to detect scope, read the installed reference
($HOME/.claude/skills/atomic-wiki/references/<scope>.md), and execute —
caller-context interface (mode/first_run/changed_range) preserved.
/refresh-signals removed (template + rendered + embedded). Bundle
regenerated with the new references.
Workstream D (CP1+CP3) of signals-wiki unification.
Three-case detection: not-a-repo + wiki/ -> realm; repo + no wiki/ -> repo; repo + wiki/ -> ask (default repo on cancel). Writes the machine-managed <wiki-type> block into claude.local.md if present else CLAUDE.md; idempotent (replace in place). Lets the inferrer/skill-router detect scope without guessing. Workstream D (CP5) of signals-wiki unification.
…ripple wiki.go classifyMembers now classifies a member repo as indexed by docs/wiki/index.md (new, primary) OR .claude/project/signals.md (legacy, back-compat) — realm scans detect both migrated and un-migrated members. doctor fix.go @-ref block heading renamed to 'Project wiki'. README, docs/reference/*, and design/spec surfaces ripple /refresh-signals -> /refresh-wiki and atomic-signals-inferrer -> atomic-wiki-inferrer (historical rename descriptions keep the old name where accurate). Workstream D (CP6) of signals-wiki unification.
One refresh verb, one inferrer agent, one skill-router.
- /refresh-signals folded into /refresh-wiki (single verb, repo + realm
via <wiki-type> detection)
- atomic-signals-inferrer renamed to atomic-wiki-inferrer (+ authoritative
docs/wiki/CLAUDE.md steering clause)
- atomic-wiki skill is a thin router; per-scope pipelines in
skills/atomic-wiki/references/{repo,realm}.md (read from the installed
$HOME/.claude location at runtime)
- atomic-setup writes the <wiki-type> scope marker
- wiki.go realm detection recognizes docs/wiki/index.md (+ legacy)
- README, docs/reference, CLAUDE.md ripple
The committed docs/wiki/scan.md is the canonical incremental-diff baseline (git diff HEAD -- docs/wiki/scan.md); tmp/.scan.prev.md is a no-git fallback. New Step 2b decision tree picks full vs incremental: no index.md -> full; <scan-sha> tiebreaker (committed scan.md blob sha != stored last-infer sha) -> full; large delta -> full; else incremental scoped to changed paths. Agent gains an optional scope: incremental|full caller override. No new staleness mechanism — reconciles with atomic signals stale and changed_range. Workstream E of signals-wiki unification.
SPA fallback serves the embedded dist for every non-API, non-carried GET; layout.html, search_page.go (minus relocated normalizeSearchSrc), the old assets/ dir, htmx.min.js, and all HTML-fragment handler paths and tests are deleted; renderers emit plain hrefs; app.css pruned of htmx selectors; graph-gates retargeted to the React shell (10/10 via the restored #btn-graph). Fixes two latent frontend bugs surfaced by the harness: null nav-group items crash and AtomicGraphUI never being installed.
Reference, atomic-serve spec (spec-currency amendment with Superseded line), and serve wiki domain file rewritten to the shipped SPA truth; corrects the graph-live-reload overstatement.
Playwright screenshot sweep of every screen surfaced six launch bugs: the code modal rendered permanently (hardcoded .open class + Ark keeping closed content mounted under .code-modal-box's display:flex — now lazyMount/unmountOnExit + state-driven class); the SPA landing hardcoded README.md, unreachable realm index (/api/page/ now resolves the landing server-side); /code/schema 500-flashed at realm roots (fetch now waits for member resolution); the editorial fonts (Newsreader/Inter/JetBrains Mono) were never carried into index.html; every page lacked the page-content-inner width/padding wrapper; and the palette's Combobox.Positioner floated results over the footer (now in-flow).
Groups (Realm/Repos/Knowledge/...) become top-level TreeView branches — collapsible with chevrons, expanded by default — instead of static headings over per-group mini-trees; restores the pre-cutover summary.nav-group visual contract on the branch controls.
…yout Rail/breadcrumb tolerate Go nil-slice JSON nulls (server now emits [] too — the null crash on link-less pages); left nav gains VSCode-style file icons and indent guides; /api/external memoized by realm fingerprint (6s walk now cached) and the page groups entries by domain; rail properties stack key-over-value instead of the cramped two-column split; markdown tables scroll horizontally inside the content column.
Extension-routed glyphs from the tree-shakeable @FortAwesome icon-data packages (brands markdown, solid file-code/image/csv/pdf/lines, folder for directory targets) rendered via a plain svg — no icon font, no react wrapper; FileIcon ships as the first ui/ barrel primitive.
Ark's Combobox.Root wrapper div broke the modal's flex column, leaving the results list unconstrained — the wrapper now participates in the column (flex:1, min-height:0) so .search-results scrolls inside 70vh.
Each member mirrors the Buckets pattern: an index leaf (the landing target) plus nested subtrees of the member's docs/ markdown and the realm-side wiki/repos/<name>/ pages; members with nothing to expand stay flat leaves.
Deep-nested entries no longer wrap into tall slivers — nav items and branch labels are nowrap with 120px minimum label room, and #nav-pane scrolls horizontally to reveal the overflow.
Member-repo docs authored against a different nesting depth (e.g. ../../../src/x.ts from gui/docs/wiki/) climb past their true target; repairOverClimbedRelative strips the ../ run and probes the remainder against each ancestor of the page's directory, deepest first. Applied in both resolveMarkdownLink (rail edges) and resolvePageHref (body hrefs) so the two stay in agreement; genuinely dead targets stay broken.
…tialiasing Hover highlight/dim, the preview card, and node drag now engage only while Shift is held — plain mouse is pan/zoom + click, so dense zoomed regions pan instead of grabbing nodes and the graph no longer fades on every mouse pass. On-canvas hint added; graph-gates harness updated to hold Shift for its drag/hover gates. Vendored cosmos point shader patched (documented in provenance): the fixed 0.9 smoothing band gave ~0.2px of edge AA at 8-14px points — visibly jagged circles. Replaced with fwidth()-based one-pixel band.
… switch crash) Points now shrink with zoom-out — pointSizeScale ramps linearly from full size (at 2.5x the mount's fit zoom) down to a 4px floor, anchored per-dataset like the zoom floor; hit targets scale with it since the same uniform feeds the GPU pick passes. The Docs|Code switch insertBefore crash was graph-core removing the React-owned loading <p> (clearLoading), corrupting React's sibling anchors for the keyed mount container. clearLoading now hides instead of removing (resetLoading re-shows per mount), and legend + hint mount into the keyed graph container — destroyed wholesale on switch — not #main-pane. Gate harness waits for the loading element hidden, not detached.
With Shift held, the first click on a node pins its neighborhood highlight — it survives mouse-out and Shift release so relationships can be studied hands-free; a second Shift-click on the same node opens its modal. Plain click still opens directly. Unpinned by background click, pinning another node, or legend-hiding the pinned type. applyHighlightState() is the single resolver (pin > shift-hover > clear); transient hover/edge highlights fall back to the pin instead of clearing. debugState() exposes pinned/hover/shift for probes.
F-1 apiSearchStreamCodeEvent comment aligned with behavior (Results always populated). F-2 root Makefile gains a frontend delegate. F-3 SearchPalette and CodeModal fetch per-branch with typed generics — the union-generic-then-cast pattern is gone. F-4 /api/code/schema returns 200 + degraded on a not-indexed member instead of 500 (soft-state convention; spec contract row amended, frontend renders the message). F-5 realm-self-index scenarios ported from the deleted htmx tests to JSON assertions (api_code_realm_test.go).
serve.md: document the Shift-gated graph interaction model (camera by default, Shift for highlight/drag, Shift-click pin then open) and zoom-scaled node sizes, in both the docs- and code-graph sections. contributing.md: pre-commit hook is four stages (frontend dist rebuild added) and a new section covers the Bun workspace, the committed embedded dist, and the make frontend / bun test / CI drift gate.
feat!(serve): React + TypeScript SPA frontend, replacing the htmx shell
Concepts gains the resolution-ladder section; getting-started a pi setup note; install the auto-migration behavior; README a multi-harness row; conventions the harness-relative path caveat.
String literals in host code naming SQL objects (Kysely selectFrom,
GORM Table, mapping declarations, annotations) previously produced no
graph edge to the .sql-defined object. Identifier-shaped literals are
now harvested as speculative refs and matched at resolution time
against indexed tables/views/procs/SQL functions -> references edges
with provenance string-match and confidence in Edge.Metadata. A 28-name
query-builder/declaration-DSL callee vocabulary (CalleeExpr, Go/TS/
Python harvesters) upgrades confidence; columns match only anchored
(qualified table.col, or bare names scoped to a function's matched
table). A fragment tier tokenizes builder-arg SQL fragments
(where("name = ?"), order-DESC, comma lists) and resolves tokens one
confidence notch lower. Unmatched refs are deleted; nodes are never
minted from strings.
Validated on taxgentic (2836 edges) and an 18-language probe corpus.
Known limits documented: no view-column nodes; Elixir/Erlang harvest
deferred (follow-up filed).
[pi.agent.<name>] model/thinking overrides merge global + repo config (repo wins per field) into a versioned JSON envelope with structured diagnostics, so the Pi agent reads tiers through the binary instead of parsing TOML itself. [pi] is opaque to unrelated config writes.
* fix(ci): install bun in test job and isolate frontend test state go generate now runs the bun frontend build (frontend_dist.go), but the test job never installed bun -> every next push failed at Generate bundle. Two flaky frontend tests were cross-file module-state leaks: window.__railCy left registered by MiniGraph.test.tsx, and loadScript's promise cache poisoned with a rejected entry by Rail/Page suites. Per-file afterEach resets plus a central reset in setup.testing.ts. * fix(ci): deterministic Rail script-load stub and spec S5 table shape The Rail suite relied on happy-dom rejecting vendor script loads synchronously — an implementation detail that doesn't hold on CI, where the unstubbed MiniGraph load chain rode past the 5s test timeout. Stub script creation + cytoscape factory for the whole suite; count only /rail/ fetches in refetch assertions. Also reshape the sql-string-match spec checkpoint table to the S5-required columns. * fix(ci): mock MiniGraph in Rail suite; strip PATH in profile subprocess test Strategist RCA: the Rail timeout was macrotask-timer starvation — RTL's own 1s waitFor timer never fired — caused by unmounting MiniGraph while its FetchEngine request (retry+dedupe, no AbortController) was inflight. Rail tests only assert panel state, so MiniGraph is mocked out (covered in its own suite); page.resolved emits act-wrapped; CP2 script-stub scaffolding removed. Profile subprocess test strips PATH so detectors probe no real tools — bazel's cache writes into the temp HOME raced t.TempDir cleanup on CI.
Adds an optional per-agent effort (low/medium/high/xhigh/max) alongside model under a harness-namespaced [claude.agents.<name>] block, applied to the installed agent frontmatter at install time and immediately on 'atomic config agents'. model accepts a tier alias or a bare Claude Code model id; validation is lenient. Drift between config and installed agents is detected by the existing doctor install-integrity check and repaired by 'atomic doctor --fix'. pi's block is renamed [pi.agent] -> [pi.agents] for symmetry (config key only; applying pi overrides stays the pi extension's job). No back-compat shim: neither block had shipped in a release.
… verbs Buckets now carry a code-generated ## Docs listing of their own topics, and the realm index a ## Buckets listing of every bucket, both spliced into XML-delimited managed regions (<bucket-docs>, <wiki-bucket-list>) so user prose around them survives regeneration. Listings derive from a six-key frontmatter contract (title, type, description, tags, status written by the author; created stamped at scaffold time); frontmatter-free files still list under ### Unindexed. atomic wiki scan rebuilds every region non-fatally. New verbs: atomic wiki bucket doc <bucket> <slug> [--router] scaffolds a topic (router adds a <slug>/ subtree for breakout subtopics), skill <bucket> scaffolds a per-bucket .claude/skills/<bucket>-management/ skill, index [<bucket>] forces a rebuild. Adds a shared managed-region splice primitive and migrates the legacy HTML-comment-bounded ## Members section onto it (position-preserving, skips on an unpaired marker rather than risk a half-migrated document).
* fix: stop C5 @-ref check flagging email domains validate config C5 parsed the domain half of any user@host.tld in CLAUDE.md prose as an @-ref and FAILed on it not resolving. Guard on the char preceding @: skip when it's an email local-part character. RE2 has no lookbehind, so the check runs at match time. Refs #159 * fix: redact PII in /report-issue before posting Both report-issue commands reproduced pasted context verbatim into a public GitHub issue — issue #159 itself leaked real emails and a domain. Add a shared privacy partial: scrub PII, secrets, and third-party identifiers to placeholders while keeping technical signal, and preview the full body for explicit confirmation before gh issue create. Refs #159 * chore(signals): refresh after #159 fixes
* fix(wiki): resolve summary repo dir from scan block atomic wiki stale reconstructed a member's directory from its summary file's own path, which never stripped .md and discarded any parent directory of the member. The derived path did not exist, git rev-parse failed, and the fail-safe branch emitted STALE summary before the reflects_rev comparison was ever reached — so three of the four member-location x summary-layout shapes could never report fresh, and affected realms stayed permanently dirty. Resolve each summary back to its Member and use Member.Path, the value scan recorded. Falls back to base-name matching for members that have graduated to indexed and carry an empty SummaryPath alongside a leftover summary file; anything still unresolved reports stale as before. Fixes #157 * chore(signals): refresh after wiki-stale-summary-resolution
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v6 breaking release: 136 commits on
next.Breaking
~/.claude/.atomic/→~/.atomic/; automatic first-run migration (rename + compat symlink). (Make CLI-managed paths configurable; move user state to ~/.atomic #150).claude/worktrees/(Claude Code's native home).atomic-commit→atomic-git-discipline,atomic-prose→atomic-writing,atomic-setup→setup-wiki,atomic-improve→retrospective-learning. (Rename four artifacts: atomic-commit, atomic-prose, atomic-setup, atomic-improve #124)Harness-agnostic paths (#150)
harness.dirconfig key routes all repo-local state (.pi/...vs.claude/...).ATOMIC_HARNESSenv >PI_CODING_AGENT=true>CLAUDECODE=1> config > default — mixed Claude/pi machines work with zero config.@-refs.Features
/quick-fix— implement→review loop without the planning phase.atomic repo init— idempotent.claude/scaffolding with nested.gitignore.atomic template <name>— document skeletons for the authoring commands..claude/atomic.tomlignore globs for the code-intel index (+ doctor category 13).Merging triggers release-please for the major bump (
feat!/fix!commits present).