@theglitchking/semantic-memory 1.2.1 → 1.5.0

package/.claude-plugin/marketplace.json

@@ -5,14 +5,14 @@
     "email": "theglitchking@users.noreply.github.com"
   },
   "metadata": {
-    "description": "Single-plugin marketplace for semantic-memory — the unified memory-layer plugin. v1.1.0 absorbs brain's strengths: AGENTS.md contract artifact, hard-gated verification sessions, multi-agent skill bundler (codex/copilot/pi), and SessionStart drift detection — all backwards-compatible with v1.0.x via deprecation shims.",
-    "version": "1.2.1"
+    "description": "Single-plugin marketplace for semantic-memory — the unified memory-layer plugin. v1.1.0 absorbs brain's strengths: AGENTS.md contract artifact, hard-gated verification sessions, multi-agent skill bundler (codex/copilot/pi), and SessionStart drift detection. v1.3 adds confidence decay — age-aware retrieval ranking with verify_note to reset the clock. All backwards-compatible with v1.0.x via deprecation shims.",
+    "version": "1.5.0"
   },
   "plugins": [
     {
       "name": "semantic-memory",
-      "description": "Unified memory-layer plugin for Claude Code. One MCP server, 40 tools across multi-corpus search/read/write/graph/lint/sessions/contract. v1.1.0 adds: AGENTS.md contract artifact, hard-gated verification sessions (session_start/run/finish/status), proposal-mode synthesize_note + synthesize_promote, multi-agent skill bundler (codex/copilot/pi via the new `skills` CLI), and SessionStart drift detection. Backwards-compatible with v1.0.x — every previous tool name remains callable through deprecation shims (removed in v2.0.0).",
-      "version": "1.2.1",
+      "description": "Unified memory-layer plugin for Claude Code. One MCP server, 44 tools across multi-corpus search/read/write/graph/lint/sessions/contract. v1.1.0 adds: AGENTS.md contract artifact, hard-gated verification sessions (session_start/run/finish/status), proposal-mode synthesize_note + synthesize_promote, multi-agent skill bundler (codex/copilot/pi via the new `skills` CLI), and SessionStart drift detection. v1.2 completes the hygiene line: `/healthcheck --fix` auto-remediation, `lint_vault({checks:['code_symbols']})` code-path drift, and a fresh-install CI smoke gate. v1.3 adds confidence decay: age-aware search ranking (0.5^(age/half-life), type-aware, floored, composes with load_priority), a `decay` block surfaced on decayed results, `verify_note` to reset the clock, `evergreen` opt-out, and `decay-config`/`decay-trace` CLI introspection. v1.3.1 adds local-only selection-logging telemetry (which note each search result actually got used), the `decay_candidates` lint, and a `selection-stats` CLI. v1.4.0 is the resident-expert bridge: a learned human→artifact lexicon (`manage_lexicon`) with propose-and-confirm alias capture, verbatim symptom capture + symptom-keyed indexing (terse symptom queries match the note), Tier-1 lexicon query expansion in the hook, archive path-class down-weight, injection hygiene (score-gate + dedup + top-3 + compact instructions), section-targeted `read_note`, and opt-in conditional tool registration. v1.5.0 is the expert-character layer: entity dossiers (`manage_dossier`) — per-component living notes (purpose / failure modes / knobs / incident log / current state) that accrete in place, with two-hop retrieval (utterance→entity→dossier injected first); usage-feedback ranking that boosts repeatedly-cited notes (capped, composes with decay/path-class) plus a `decoys` lint for retrieved-but-never-cited notes (surfaced, never auto-down-ranked); session paging (Stop drafts a durable session digest as a proposal, SessionStart pages in a curated digest instead of a broad sweep); and a speaker profile (`manage_profile`) that models how the human communicates — severity calibration, chronic omissions, verbosity, shorthand — injected at SessionStart. Backwards-compatible with v1.0.x — every previous tool name remains callable through deprecation shims (removed in v2.0.0).",
+      "version": "1.5.0",
       "author": {
         "name": "TheGlitchKing"
       },

package/.claude-plugin/plugin.json

@@ -1,14 +1,14 @@
 {
   "name": "semantic-memory",
   "description": "Unified memory-layer plugin for Claude Code. One MCP server, multiple typed corpora (vault / code / plans / docs / research / project-map), unified cross-corpus knowledge graph, conditional tool registration, in-process drift detection, and human↔code translation. Rebrand of `semantic-sidekick` at v1.0.0 — see CHANGELOG for migration.",
-  "version": "1.0.1",
+  "version": "1.5.0",
   "author": {
     "name": "TheGlitchKing",
     "email": "theglitchking@users.noreply.github.com"
   },
   "license": "MIT",
-  "homepage": "https://github.com/TheGlitchKing/semantic-sidekick",
-  "repository": "https://github.com/TheGlitchKing/semantic-sidekick",
+  "homepage": "https://github.com/TheGlitchKing/semantic-memory",
+  "repository": "https://github.com/TheGlitchKing/semantic-memory",
   "keywords": [
     "mcp",
     "memory-layer",

package/CHANGELOG.md

@@ -2,6 +2,150 @@
 
 All notable changes to semantic-memory (formerly semantic-sidekick) will be documented here.
 
+## [1.5.0] - 2026-07-11 — Expert-character layer (v1.5.0: Phases 8–11)
+
+Where v1.4.0 taught the plugin *how this human talks about the system*, v1.5.0 gives it the other two traits of a resident expert: it organizes memory by **component** (not by file) and **learns from its own usage**. Tool surface 42 → 44 (`manage_dossier`, `manage_profile`; read-only unchanged at 21). Additive throughout; `usage_boost.enabled: false` reproduces byte-identical pre-v1.5 ranking.
+
+### Added
+
+- **Entity dossiers** (`src/core/dossier.ts`, **`manage_dossier`**). Per-component living notes at `<vault>/dossiers/<slug>.md` (`dossier` note type) with fixed sections — Purpose / Failure modes / Knobs & commands / Incident log / Current state. Knowledge accretes **in place** (incidents append, current-state is revised; never a new note per event). `manage_dossier` actions: `init | append_incident | set_state | get | list`. CLI: `semantic-memory dossier init <entity> [--alias …] [--seeded-from …]` / `dossier list`. Dossier `aliases:` fold into the lexicon compiler so Tier-1 expansion routes to them.
+- **Two-hop retrieval** (`resolveDossierForPrompt` + `formatDossierHead` in `vault-context.js`). When an utterance names a tracked entity/alias, the dossier head (Purpose + Current state + a read-the-Incident-log pointer) is injected **first**, ahead of semantic hits — utterance → entity → dossier. Finally makes the graph load-bearing at query time.
+- **Usage-feedback ranking** (`src/core/usage-boost.ts`, `applyUsageBoost`). Consumes the v1.3.1 selection log: repeatedly-cited notes earn a bounded boost `min(cap, 1 + citations·per_citation)` (default `cap: 1.5`, `per_citation: 0.1`, `usage_boost` block in `vault.schema.yml`), composed **multiplicatively** with decay + path-class + `load_priority` at the shared `context.ts` rank site. TTL-cached (15s) citation snapshot; boosted results carry a `usage: {citations, multiplier}` block. The cap stops a feedback runaway.
+- **Decoys lint** (`findDecoys`, `lint_vault({checks:["decoys"]})`). Notes retrieved 3+ times but never cited are **surfaced for review, never auto-down-ranked** — down-rank on evidence, never on ambiguous inference (decision Q5).
+- **Session paging.** Stop: the session-close prompt drafts a durable digest (decisions / resolutions / task-state) via `synthesize_note` as a reviewable **proposal** (`proposal_subdir: "sessions"`), graduated by `synthesize_promote` (decision Q10). SessionStart: `buildSessionStartDigest` pages in a curated block (active task + last session digest + dossier current-states + mode) instead of a broad whole-vault sweep when there's durable state; falls back otherwise.
+- **Speaker profile** (`src/core/profile.ts`, **`manage_profile`**). `profile` note type at `<vault>/profile/speaker.md` (evergreen), fixed sections — Severity calibration / Chronic omissions / Verbosity preference / Shorthand & terms. Injected at SessionStart (`<vault-speaker-profile>`, capped, silent until filled). `manage_profile` actions: `init | get | update_section`. CLI: `profile init|show`. Updated via a correction cue ("when I say X I mean Y") folded into the existing capture-cue machinery, routed to `manage_profile` rather than `synthesize_note`. One human, one profile.
+
+### Decisions (locked at kickoff, 2026-07-11)
+
+Q5 — decoys stay lint-only. Q9 — conditional tool registration stays default OFF (`tools/list_changed` reliability unverified). Q10 — session digest is an automatic draft filed as a proposal. Q11 — learned aliases stay propose-and-confirm regardless of `evidence_count`.
+
+### Tests
+
+- New: `dossier`, `two-hop-dossier`, `usage-boost`, `lint-decoys`, `profile` unit suites; `dossier-mcp`, `usage-boost-ranking`, `profile-mcp` integration; `phase10/session-paging`, `phase11/speaker-profile` hook suites. Regression shape snapshots made citation-independent.
+- Tool counts 42 → 44 (read-only unchanged at 21). Golden eval: zero regression (recall@1=86% recall@3/@5=100% MRR=0.929). **418 tests green; fresh-install smoke PASS.**
+
+## [1.4.0] - 2026-07-10 — Resident-expert bridge (v1.4.0: Phases 1–7)
+
+The human→LLM bridge arc: learn how *this human* talks about the system, map that phrasing to concrete artifacts, and pay down the plugin's own token overhead. Tool surface 41 → 42 (`manage_lexicon`). Additive throughout; default ranking behavior is unchanged except for the new archive down-weight (opt-out).
+
+### Added
+
+- **Golden retrieval eval harness** (`test/retrieval-eval/`, `npm run eval`). Pure metrics engine (recall@k, MRR, per case-class) + a class-tagged golden set driven through the real `search_semantic` stack. The measurement foundation — every ranking/expansion change now shows a delta. Baseline captured at recall@1=86%, MRR=0.929.
+- **Path-class ranking** (`src/core/path-class.ts`). `archive/**` → 0.3× down-weight (configurable via `path_class` in `vault.schema.yml`), composed multiplicatively with decay + `load_priority` at the same rank site. Directly fixes retired-doc copies dominating results.
+- **Injection hygiene** in `formatContextBlock` (the `<vault-context>` render point): score-gates weak prompts (`SEMANTIC_MEMORY_INJECT_MIN_SCORE`, default 0.35), dedupes archive twins by basename, caps at top-3, and shrinks the instructions from ~150 to ~45 words — cutting per-prompt token overhead at the source while preserving the cite-or-deflect scoping.
+- **Lexicon corpus** — learned human→artifact aliases. `alias` note type under `<vault>/lexicon/`, a derived `lexicon-cache.json`, and **`manage_lexicon`** (`action: add|lookup|list|remove|compile`, one tool). CLI: `semantic-memory lexicon list|compile|add`. Repeat observations bump `evidence_count` + confidence.
+- **Alias capture loop** — propose-and-confirm: a `vault-first` skill instruction offers a `manage_lexicon add` when the LLM resolves the user's vague phrasing to a concrete artifact (never auto-adds). Conflict detection via opt-in `lint_vault({checks:["alias_conflicts"]})` (a phrase mapping to >1 target is surfaced, never auto-resolved).
+- **Verbatim symptom capture + symptom-keyed indexing.** `synthesize_note` gains a `symptoms` param → `symptoms:` frontmatter; the indexer adds each verbatim symptom phrase as its own chunk pointing at the note (synthetic child chunks, no index-format change). A note surfaces on a terse symptom query even when its prose never uses those words — the asymmetric-retrieval fix.
+- **Query expansion (two tiers).** Tier 1 (deterministic, in `vault-context.js`): `expandQueryViaLexicon` appends alias canonical targets to a user utterance before embedding. Tier 2 (LLM-side): a `vault-first` instruction to rewrite a terse utterance with conversation context and re-search once before concluding "not in vault".
+- **Token-frugal tool surface.** `read_note` gains a `section` param (return one heading's section, not the whole file). Conditional tool registration (`tools.conditional` in `vault.schema.yml`, **default OFF** per the risk of mid-session mode switches): when enabled, outage-silence mode registers only the core search/read surface.
+
+### Deferred within the arc (documented)
+
+Near-duplicate collapse at index time (injection-layer basename dedup covers the observed case), rolling-topic query expansion (`topic.json` — start dumb, KQ7), and compact-search-output as the default shape. v1.5.0 (dossiers, usage-feedback ranking, session paging, speaker profile) is the next arc.
+
+### Tests
+
+- New unit suites: eval-metrics, path-class, injection-hygiene, lexicon, lint-alias-conflicts, query-expansion, section, tools-config. New integration: symptom-keyed retrieval, archive down-weight, section reads, conditional registration. Golden eval wired into `npm run eval`.
+- Tool-surface + output snapshots updated additively (manage_lexicon; alias_conflicts enum/byRule; read_note `section` + synthesize_note `symptoms` params). Tool counts 41 → 42 (read-only unchanged at 21). **371 tests green; fresh-install smoke PASS.**
+
+## [1.3.2] - 2026-07-10 — Fix hook double-registration (double vault-context injection)
+
+### Fixed
+
+- **`vault-context.js` no longer fires twice per prompt.** On a plugin install the plugin's own `hooks/hooks.json` registers SessionStart/UserPromptSubmit/Stop — but this repo's committed `.claude/settings.json` *also* registered the same three events (legacy dogfooding scaffolding from the Phase 2 era, before the plugin was marketplace-installable). With the plugin enabled, both sources fired, so `vault-context.js` ran twice and the `<vault-context>` block was injected **twice on every prompt** (~1.5k tokens of duplicated overhead per turn). Removed the redundant `hooks` block from `.claude/settings.json`; the plugin's `hooks/hooks.json` is now the single source of truth.
+
+### Added
+
+- **`hook_double_registration` healthcheck finding** (fast tier). Detects the same hook event declared in BOTH `.claude/settings.json` and the plugin's `hooks/hooks.json` and warns that each hook fires twice, pointing at the fix. Only fires in a plugin context (`CLAUDE_PLUGIN_ROOT` present); a silent no-op for npm-dependency installs, which legitimately register via `settings.json`. This is the durable guard so the double-injection can't silently recur on any install — the item flagged as v1.4 Phase 0.
+
+### Tests
+
+- New: `test/unit/healthcheck-double-hook.test.ts` (warns on overlap; no-op without `CLAUDE_PLUGIN_ROOT`; no warn on disjoint events). 331 tests green.
+
+## [1.3.1] - 2026-07-10 — Selection-logging telemetry (the v1.4 precursor)
+
+Ships the two pieces deferred out of v1.3.0 so retrieval can learn from its own outcomes. v1.3.1 only **observes** — there is no ranking change (usage-feedback ranking is v1.4). Strictly local, append-only, opt-out.
+
+### Added
+
+- **Selection logging** (`src/core/telemetry.ts`) → `.claude/.semantic-memory/selection.jsonl` (local, append-only JSONL, gitignored, never leaves the machine). Two event kinds: a `search` event (`{tool, query, results:[{path, score, decay?}]}`) logged by `search_semantic`/`search_hybrid` — reusing the decay multiplier already computed — and a `selection` event (`{note_path, via, correlated}`) logged by `read_note`. `correlated: true` marks a read that followed a search which returned that path (best-effort, 60s in-process window). Awaited so the signal is durable; `appendEvent` never throws and respects the opt-out, so it can never fail the tool. Config: `telemetry.enabled` in `vault.schema.yml` (default true; `false` disables all logging). **No network** — enforced by a unit test that greps the module.
+- **`lint_vault({checks:["decay_candidates"]})`** — new opt-in lint rule. Cross-references the selection log (notes that appeared in recent search results) against each note's current decay multiplier, and flags notes retrieved frequently but decayed to ≤0.5 ("retrieved N× recently but decayed to M — verify_note or revise"), sorted most-retrieved first. Index-free (no embedder); a silent no-op when there's no selection log. Never in the default report, same as `code_symbols`.
+- **`semantic-memory selection-stats --notes <path>`** — CLI rollup of the log: searches, selections, most-cited notes, and retrieved-but-never-cited notes (`--json` for raw).
+
+### Fixed
+
+- **`regenerate_contract` no longer hardcodes the contract version** (`src/mcp/tools/contract.ts` had `pluginVersion: "1.1.0"` frozen, so AGENTS.md was stamped 1.1.0 on every regeneration — the same class of freeze bug as the `plugin.json` fix in 1.2.2). Now resolves the real version by walking up from the module's runtime location to the package's own `package.json` (matched by name), robust to tsup bundling/splitting. (Landed on main ahead of this release; AGENTS.md was regenerated to 1.3.0.)
+
+### Deferred (still, to v1.4+)
+
+- Backlink hotness (wired but flag-off) and the **usage-feedback ranking** that consumes this log — the latter is v1.4 Phase 9. v1.3.1 deliberately produces the signal without acting on it, so the log can accumulate real data before ranking tunes against it.
+
+### Tests
+
+- New: `test/unit/telemetry.test.ts` (append/read, opt-out, fire-and-forget-never-throws, correlation window, stats rollup, no-network grep); `test/unit/lint-decay-candidates.test.ts` (flags retrieved-but-decayed, spares fresh, opt-in gating, no-log no-op).
+- Extended: `test/integration/mcp-server.test.ts` (search→read lands both events; the selection is `correlated`).
+- Updated: tool-surface + tool-output regression snapshots (additive `decay_candidates` enum value + byRule key). 328 tests green.
+
+## [1.3.0] - 2026-07-10 — Confidence decay: age-aware retrieval ranking
+
+Replaces age-blind ranking with smooth, type-aware confidence decay. Notes age out of relevance gracefully; explicitly-verified notes reset the clock; agents see decay state and can re-verify. Opt-out via one config line.
+
+### Added
+
+- **Decay engine (`src/core/decay.ts`).** Pure, side-effect-free: `multiplier = 0.5^(age_days / half_life)`, keyed on time since `last_verified`. Per-type half-life (`decision`/`note` 365d, `gotcha` 180d, `source` never, `proposal` 14d), floored at 0.1 (notes down-weight, never disappear). Fails open (multiplier 1.0) on any uncertainty — disabled config, missing/invalid/**future** `last_verified` — so decay can only down-rank a note we're confident is old.
+- **Decay applied at search time.** `search_semantic` and `search_hybrid` multiply decay into the score after the existing `load_priority` boost (composes, never replaces). `search_text` (exact-match intent) and `search_graph` (graph distance is the signal) are deliberately unaffected.
+- **`decay` block surfaced in results.** Decayed results (multiplier < 1) carry `{ multiplier, age_days, effective_half_life, reason }`; fresh results stay clean.
+- **`verify_note` MCP tool** (tool count 40 → 41). Stamps `last_verified` to today WITHOUT touching content or any other field, logs a `verify` event, and returns the note's new decay multiplier. The explicit clock-reset.
+- **`evergreen` frontmatter.** `evergreen: true` pins a note at multiplier 1.0 while its `last_verified` is within 365 days; past that it decays normally (the evergreen claim itself expires, forcing periodic re-affirmation).
+- **CLI introspection.** `semantic-memory decay-config --notes <path>` prints the active config (defaults vs. `vault.schema.yml` override); `semantic-memory decay-trace <note> --notes <path>` prints the full calculation for one note.
+- **Config in `vault.schema.yml`.** A documented `decay:` block ships in the default schema. `decay.enabled: false` restores byte-identical pre-v1.3 ranking.
+
+### Fixed
+
+- **Unquoted-date frontmatter no longer silently disables decay.** YAML parses `last_verified: 2019-01-01` (unquoted) into a `Date`, not a string, so a naive `typeof === "string"` check dropped it and every such note read as "no last_verified (fail open)". New `normalizeVerifiedDate()` coerces string **or** Date at all read sites (search, `verify_note`, `decay-trace`). Caught by the `decay-trace` smoke test during development.
+
+### Semantics note: `last_verified` vs. edits
+
+Decay keys on `last_verified`, which is stamped only at note creation (`synthesize_note`, `ingest_source`) and by `verify_note` — **no edit path bumps it**. So ordinary edits do not reset the decay clock, which is the intended v1.3 correctness property. The separate `last_modified` frontmatter field from the original plan (Phase 2) is therefore not required for correct decay and is deferred; it can be added later for edit-recency use cases without affecting decay.
+
+### Deliberately deferred (documented, not dropped)
+
+- **Backlink hotness boost (Phase 7)** — the engine supports it (`hotness_boost` config), but it ships **flag-off by default**; hub notes (index.md) distort the signal, so it must be earned via telemetry before defaulting on.
+- **`decay_candidates` lint (Phase 8)** and **selection-logging telemetry (Phase 10)** — both need query-log history / weeks of passive collection to be meaningful, and telemetry is the dependency for the v1.4 usage-feedback ranking. Staged as a v1.3.x follow-up.
+
+### Tests
+
+- New: `test/unit/decay.test.ts` (12 cases — half-life curve, floor, per-type, never-decay, fail-open, evergreen + expiry, hotness, Date-normalization regression).
+- Extended: `test/integration/mcp-server.test.ts` (verify_note round-trip; `search_semantic` attaches a `decay` block to an old-`last_verified` note).
+- Updated: tool-surface regression snapshots (additive `verify_note` tool + decay-aware search descriptions); tool-count assertions 40 → 41 (read-only mode unchanged at 21 — `verify_note` is write-gated).
+
+## [1.2.3] - 2026-07-10 — Complete the v1.2 hygiene line: `--fix`, code-symbol drift, CI smoke
+
+Ships the three v1.2 roadmap items that slipped when 1.2.1/1.2.2 were preempted by defect fixes. All three are additive; no tool is removed and default behavior is unchanged unless a flag is passed.
+
+### Added
+
+- **`healthcheck --fix` — auto-remediation of safe drift.** `/healthcheck --fix` (and the `semantic-memory healthcheck --fix` CLI) now applies **safe, idempotent, non-destructive** fixes for fixable findings and re-runs drift detection to show the post-fix state. Actions: re-link skills (`skill-link`), reconcile `.mcp.json` (`mcp-reconcile`), reindex the vault (`reindex`), and migrate legacy state (`state-migrate`). Findings that touch user-authored content — stale notes, broken wikilinks, hand-edited `AGENTS.md` — are reported for human review, never auto-changed. The decision logic lives in a pure, unit-tested planner (`src/core/healthcheck-fix.ts`); the CLI executes the plan. The `legacy_state_files` finding's `fixable_via` changed from `none` to `state-migrate`.
+- **`lint_vault({checks: ["code_symbols"]})` — code-path drift detection.** New opt-in lint rule: scans note inline-code spans for repo-relative file-path references and flags ones whose first segment IS a real directory in the repo but whose full path no longer exists (a stale reference to a moved/deleted file). Anchoring on an existing first segment keeps false positives low — paths belonging to other repos are skipped. Fails open (silent no-op) outside a code repo. **Opt-in only:** never part of the default `lint_vault` report or the healthcheck slow tier, so existing behavior is byte-stable. Scope note: this validates *path* references; fine-grained symbol-name checking needs a real symbol index and is deferred to the v1.4 lexicon arc, which will extend this same `code_symbols` rule.
+- **Fresh-install CI smoke test.** New `scripts/smoke-install.sh` + `.github/workflows/ci.yml` `smoke` job: `npm pack` → install the tarball into a throwaway consumer project → assert (1) `bin --version` reports the current version, (2) the CLI loads all subcommands, (3) every runtime file is actually in the tarball, and (4) the SessionStart `reconcile` wiring populates `.mcp.json` on a fresh install. This mechanically prevents the v1.1.0-class packaging bug (the highest-ROI item on the v1.2 roadmap).
+
+### Fixed
+
+- **Drift detection now runs on healthy installs.** The `healthcheck` CLI command called `process.exit(0)` immediately after the install smoke-test succeeded, so the drift-detection `postAction` hook (added in v1.1) never ran on a clean install — it only surfaced when the smoke-test failed. The command is now a single coherent action: smoke-test → drift → optional `--fix` → emit, exiting once at the end. The `formatDriftBanner` line advertising `/healthcheck --fix` is no longer a promise for a flag that doesn't exist.
+
+### Tests
+
+- New: `test/unit/healthcheck-fix.test.ts` (planner: safe-action mapping, human-review routing, ok-finding filtering).
+- New: `test/unit/lint-code-symbols.test.ts` (drift on a stale path, no-flag on an existing path, other-repo skip, URL/glob rejection, opt-in gating, fail-open outside a code repo).
+- Updated: tool-surface regression snapshots (additive `code_symbols` enum value + description on `lint_vault`).
+
+## [1.2.2] - 2026-06-27 — Plugin-aware hook-registration check + manifest version sync
+
+### Fixed
+
+- **`hook_registration` drift no longer false-positives on plugin-style installs.** The check (both the SessionStart fast path in `hooks/vault-context.js` and the CLI `checkHookRegistration` in `src/core/healthcheck.ts`) only inspected the project's `.claude/settings.json`. When semantic-memory is installed as a Claude Code plugin, its SessionStart/UserPromptSubmit/Stop hooks live in the plugin's own `hooks/hooks.json` (resolved via `CLAUDE_PLUGIN_ROOT`) and fire correctly, so the check warned about "missing" hooks that were in fact registered. Both sites now treat events declared in the plugin's `hooks/hooks.json` as registered. Npm-dependency installs (no `CLAUDE_PLUGIN_ROOT`) are unaffected and still require the hooks in `settings.json`.
+- **Plugin manifest version sync.** `.claude-plugin/plugin.json` was frozen at `1.0.1` while `package.json`, git tags, and `marketplace.json` advanced — Claude Code reads the plugin version from `plugin.json`, so `claude plugin update` always reported "already at latest (1.0.1)" and never pulled newer code. Bumped `plugin.json` to match, and corrected its stale `homepage`/`repository` URLs (they pointed at the old `semantic-sidekick` repo).
+
 ## [1.2.1] - 2026-06-11 — Capture-cue false-positive fixes
 
 Fixes two classes of false positives in the Stop-hook capture nudge (`hooks/vault-context.js`), where the cue scanner over-fired and asked to synthesize moments that carried no new knowledge.

package/ROADMAP.md

@@ -2,8 +2,11 @@
 
 This file tracks the committed near-term direction for `@theglitchking/semantic-memory`. It's a planning surface — not a contract. Items move between sections as the work clarifies; the canonical state lives here in git.
 
-> **Current shipped version:** [v1.1.1](https://github.com/TheGlitchKing/semantic-sidekick/releases/tag/v1.1.1) (npm `latest`)
-> **Last updated:** 2026-05-09
+> **Current shipped version:** v1.2.3 on `main` (npm `latest`); v1.3.0 (confidence-decay core) in review on `feat/v1.3-confidence-decay`.
+> **Last updated:** 2026-07-10
+>
+> **v1.2 status:** COMPLETE — state consolidation (1.2.0), `/healthcheck --fix` + `code_symbols` lint + fresh-install CI smoke (1.2.3). The three items that slipped past 1.2.0/1.2.1/1.2.2 landed in 1.2.3.
+> **v1.3 status:** core SHIPPED (decay engine, search integration, `decay` surfacing, `verify_note`, `evergreen`, `decay-config`/`decay-trace`). Deferred within the v1.3 line: backlink hotness (flag-off), `decay_candidates` lint, and selection-logging telemetry (dependency for the v1.4 usage-feedback ranking). The `last_modified` split proved unnecessary for decay correctness — `last_verified` is already never bumped on edits.
 
 ## Legend
 

package/commands/healthcheck.md

@@ -1,5 +1,5 @@
 ---
-description: Verify the local install + run drift detection. Self-heals npx-cache ERR_MODULE_NOT_FOUND. Pass --fast to skip the slow tier (full vault lint).
+description: Verify the local install + run drift detection. Self-heals npx-cache ERR_MODULE_NOT_FOUND. Pass --fast to skip the slow tier, --fix to auto-apply safe fixes.
 allowed-tools: Bash(npx:*), Bash(node:*)
 ---
 
@@ -7,18 +7,20 @@ When the user runs `/healthcheck`:
 
 - `/healthcheck` (no arg) — Run the local install verification AND the full drift check (fast tier + slow tier). Report the results: install status, drift findings (if any), and remediation pointers (e.g. `/relink`, `/normalize-config`, `regenerate_contract`).
 - `/healthcheck --fast` — Run the install verification + ONLY the fast-tier drift checks. Skips the full vault lint (slow tier). Use when the agent only wants quick install/manifest checks without the multi-second vault scan.
+- `/healthcheck --fix` — Run drift detection, then auto-apply **safe** fixes for fixable findings and report what was done. Combinable with `--fast`.
 
 The fast-tier auto-check also runs on every `SessionStart` via `vault-context.js` — healthy installs see nothing at session start, drifted installs see a one-block warning with a pointer to this command.
 
-Implementation: shell out to `node ./node_modules/@theglitchking/semantic-memory/bin/semantic-memory healthcheck [--fast]` (or `npx --no @theglitchking/semantic-memory healthcheck [--fast]` if no local install). Falls back to the legacy `@theglitchking/semantic-sidekick` package on machines mid-migration.
+Implementation: shell out to `node ./node_modules/@theglitchking/semantic-memory/bin/semantic-memory healthcheck [--fast] [--fix]` (or `npx --no @theglitchking/semantic-memory healthcheck [...]` if no local install). Falls back to the legacy `@theglitchking/semantic-sidekick` package on machines mid-migration.
 
-Drift findings are categorized by check:
-- `mcp_json_entry` — `.mcp.json` missing the semantic-memory server entry. Fix: `/normalize-config`.
-- `hook_registration` — `.claude/settings.json` missing one of SessionStart/UserPromptSubmit/Stop. Fix: `/relink` or reinstall.
-- `agents_contract` — `AGENTS.md` exists but lacks managed-block markers. Fix: move custom content to a `Local Notes` section, or delete and re-run `regenerate_contract`.
-- `session_staleness` — A session has been open >24h with no activity. Fix: resume (run `session_run` / `session_finish`) or remove the stale session file.
-- `index_freshness` — No vector index built yet. Fix: call `reindex`.
-- `skill_manifest:*` — Per-agent skill install state. Informational unless missing.
-- `lint_vault` (slow tier only) — Vault lint findings. Many require human review (stale notes, broken wikilinks).
+Drift findings are categorized by check (the `Fix?` column shows what `--fix` does automatically):
+- `mcp_json_entry` — `.mcp.json` missing the semantic-memory server entry. **`--fix`: reconciles `.mcp.json`** (also `/normalize-config`).
+- `hook_registration` — `.claude/settings.json` missing one of SessionStart/UserPromptSubmit/Stop. **`--fix`: re-links skills/hooks** (also `/relink`).
+- `index_freshness` — No vector index built yet. **`--fix`: reindexes the vault.**
+- `legacy_state_files` — Legacy `.claude/.sidekick-*` state files present. **`--fix`: runs `migrate-state`.**
+- `skill_manifest:*` — Per-agent skill install state. **`--fix`: re-links skills** when flagged.
+- `agents_contract` — `AGENTS.md` exists but lacks managed-block markers. **Not auto-fixed** (needs a human decision — move custom content to a `Local Notes` section, or delete and re-run `regenerate_contract`).
+- `session_staleness` — A session has been open >24h with no activity. **Not auto-fixed** (resume via `session_run` / `session_finish`, or remove the stale session file).
+- `lint_vault` (slow tier only) — Vault lint findings. **Not auto-fixed** — stale notes, broken wikilinks, and schema violations require human review.
 
-`--fix` flag is reserved for v1.2 — auto-applying safe fixes (re-link skills, reconcile `.mcp.json`, regenerate contract) is the planned v1.2 work. For v1.1, drift detection is read-only and points the user at the right manual command.
+`--fix` is intentionally conservative: it only applies idempotent, non-destructive fixes derivable from the install itself. Anything touching user-authored content is reported for human review, never auto-changed. After applying fixes it re-runs drift detection so the printed findings reflect the post-fix state.

package/dist/{chunk-EVAJGOCB.js → chunk-2EELGTLX.js}

@@ -1,10 +1,10 @@
 import {
   lintVault
-} from "./chunk-CAN2GWUG.js";
+} from "./chunk-FM26NFTR.js";
 
 // src/core/healthcheck.ts
 import { readFile, writeFile, mkdir } from "fs/promises";
-import { existsSync } from "fs";
+import { existsSync, readFileSync } from "fs";
 import { join } from "path";
 import { homedir } from "os";
 var CACHE_TTL_MS = 5 * 60 * 1e3;
@@ -52,6 +52,7 @@ async function runFastTier(opts) {
     checkPluginVersion(opts.projectRoot),
     checkMcpJsonEntry(opts.projectRoot),
     checkHookRegistration(opts.projectRoot),
+    checkHookDoubleRegistration(opts.projectRoot),
     checkIndexFreshness(opts.projectRoot, opts.vaultPath),
     checkSessionStaleness(opts.projectRoot),
     checkAgentsContract(opts.projectRoot),
@@ -123,6 +124,19 @@ async function checkMcpJsonEntry(projectRoot) {
   }
   return { check: "mcp_json_entry", severity: "ok", summary: ".mcp.json server entry present" };
 }
+function pluginRegisteredHookEvents() {
+  try {
+    const root = process.env.CLAUDE_PLUGIN_ROOT;
+    if (!root) return [];
+    const hooksPath = join(root, "hooks", "hooks.json");
+    if (!existsSync(hooksPath)) return [];
+    const data = JSON.parse(readFileSync(hooksPath, "utf-8"));
+    const hooks = data?.hooks ?? {};
+    return Object.keys(hooks).filter((e) => Array.isArray(hooks[e]) && hooks[e].length > 0);
+  } catch {
+    return [];
+  }
+}
 async function checkHookRegistration(projectRoot) {
   const settings = join(projectRoot, ".claude", "settings.json");
   if (!existsSync(settings)) return null;
@@ -130,10 +144,12 @@ async function checkHookRegistration(projectRoot) {
     const data = JSON.parse(await readFile(settings, "utf-8"));
     const hooks = data?.hooks ?? {};
     const required = ["SessionStart", "UserPromptSubmit", "Stop"];
+    const pluginEvents = pluginRegisteredHookEvents();
     const missing = [];
     for (const event of required) {
       const arr = hooks[event];
-      if (!Array.isArray(arr) || arr.length === 0) missing.push(event);
+      const inSettings = Array.isArray(arr) && arr.length > 0;
+      if (!inSettings && !pluginEvents.includes(event)) missing.push(event);
     }
     if (missing.length > 0) {
       return {
@@ -148,6 +164,34 @@ async function checkHookRegistration(projectRoot) {
     return failOpenWarn(err);
   }
 }
+async function checkHookDoubleRegistration(projectRoot) {
+  const settings = join(projectRoot, ".claude", "settings.json");
+  if (!existsSync(settings)) return null;
+  const pluginEvents = pluginRegisteredHookEvents();
+  if (pluginEvents.length === 0) return null;
+  try {
+    const data = JSON.parse(await readFile(settings, "utf-8"));
+    const hooks = data?.hooks ?? {};
+    const doubled = [];
+    for (const event of ["SessionStart", "UserPromptSubmit", "Stop"]) {
+      const arr = hooks[event];
+      const inSettings = Array.isArray(arr) && arr.length > 0;
+      if (inSettings && pluginEvents.includes(event)) doubled.push(event);
+    }
+    if (doubled.length > 0) {
+      return {
+        check: "hook_double_registration",
+        severity: "warn",
+        summary: `hook event(s) registered in BOTH settings.json and the plugin \u2014 fires twice: ${doubled.join(", ")}`,
+        detail: `The plugin's hooks/hooks.json already registers ${doubled.join(", ")}, so the duplicate registration in .claude/settings.json makes each hook run twice (e.g. the <vault-context> block injected twice per prompt). Remove the "hooks" block from .claude/settings.json \u2014 the plugin's hooks.json is the single source of truth for plugin installs.`,
+        fixable_via: "none"
+      };
+    }
+    return { check: "hook_double_registration", severity: "ok", summary: "no double-registered hooks" };
+  } catch (err) {
+    return failOpenWarn(err);
+  }
+}
 async function checkIndexFreshness(projectRoot, vaultPath) {
   const vault = vaultPath ?? defaultVaultPath(projectRoot);
   if (!vault || !existsSync(vault)) return null;
@@ -213,7 +257,7 @@ async function checkLegacyStateFiles(projectRoot) {
     severity: "warn",
     summary: `${present.length} legacy state file${present.length === 1 ? "" : "s"} at .claude/.sidekick-*`,
     detail: `Files: ${present.join(", ")}. Run \`bin/semantic-memory migrate-state\` to move them under .claude/.semantic-memory/. These files are still being read for backwards-compat through v1.x; the legacy fallback is removed in v2.0.`,
-    fixable_via: "none"
+    fixable_via: "state-migrate"
   };
 }
 async function checkAgentsContract(projectRoot) {
@@ -294,4 +338,4 @@ export {
   filterToDrift,
   formatDriftBanner
 };
-//# sourceMappingURL=chunk-EVAJGOCB.js.map
+//# sourceMappingURL=chunk-2EELGTLX.js.map

package/dist/chunk-2EELGTLX.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/core/healthcheck.ts"],"sourcesContent":["import { readFile, writeFile, mkdir, stat } from \"node:fs/promises\";\nimport { existsSync, readFileSync } from \"node:fs\";\nimport { join, basename } from \"node:path\";\nimport { createHash } from \"node:crypto\";\nimport { homedir } from \"node:os\";\nimport { lintVault } from \"./lint.js\";\nimport { deriveProjectRoot } from \"./session.js\";\n\nexport type Tier = \"fast\" | \"slow\" | \"all\";\nexport type Severity = \"ok\" | \"warn\" | \"error\";\n\nexport interface DriftFinding {\n  check: string;\n  severity: Severity;\n  summary: string;\n  detail?: string;\n  fixable_via?: \"skill-link\" | \"mcp-reconcile\" | \"regenerate-contract\" | \"reindex\" | \"state-migrate\" | \"none\";\n}\n\nexport interface HealthcheckResult {\n  tier_run: Tier;\n  ran_at: string;\n  duration_ms: number;\n  findings: DriftFinding[];\n  counts: { ok: number; warn: number; error: number };\n  cached?: boolean;\n}\n\nexport interface HealthcheckOptions {\n  projectRoot: string;\n  /** Vault path. When omitted, derived from projectRoot's .claude/.vault. */\n  vaultPath?: string;\n  tier?: Tier;\n  /** Cache file path. Default: <projectRoot>/.claude/.semantic-memory/healthcheck-cache.json */\n  cachePath?: string;\n  /** Force re-run even if cache is <5 minutes old. */\n  force?: boolean;\n  /** Override \"now\" — used by tests. */\n  nowMs?: number;\n}\n\nconst CACHE_TTL_MS = 5 * 60 * 1000;\n\n/**\n * Run the drift-detection healthcheck.\n *\n *  - Fast tier: cheap file-system probes (~ms each). Plugin version, skill manifests,\n *    .mcp.json registration, hook registration, index freshness, session staleness,\n *    AGENTS.md managed-block sha. All independent, run in parallel. Total budget: <100ms\n *    on a representative install.\n *  - Slow tier: full vault lint. Adds tens of seconds on large vaults — invoked by\n *    explicit /healthcheck, never by the SessionStart auto path.\n *  - Cache: when force=false and the cache file is <5min old, return the cached result.\n *\n * Fail-open: any individual check that throws produces a `severity: \"warn\"` finding\n * with the error message; never propagates.\n */\nexport async function runHealthcheck(opts: HealthcheckOptions): Promise<HealthcheckResult> {\n  const start = (opts.nowMs ?? Date.now());\n  const tier: Tier = opts.tier ?? \"fast\";\n  const cachePath = opts.cachePath ?? join(opts.projectRoot, \".claude\", \".semantic-memory\", \"healthcheck-cache.json\");\n\n  if (!opts.force && existsSync(cachePath)) {\n    try {\n      const raw = await readFile(cachePath, \"utf-8\");\n      const cached = JSON.parse(raw) as HealthcheckResult & { ran_at_ms: number };\n      if (cached.tier_run === tier && start - cached.ran_at_ms < CACHE_TTL_MS) {\n        return { ...cached, cached: true };\n      }\n    } catch {\n      // ignore corrupt cache; will overwrite below\n    }\n  }\n\n  const findings = tier === \"fast\" ? await runFastTier(opts) : tier === \"slow\" ? await runSlowTier(opts) : [...(await runFastTier(opts)), ...(await runSlowTier(opts))];\n\n  const counts = countBySeverity(findings);\n  const ranAt = new Date(start).toISOString();\n  const result: HealthcheckResult = {\n    tier_run: tier,\n    ran_at: ranAt,\n    duration_ms: Date.now() - start,\n    findings,\n    counts,\n  };\n\n  // Persist cache (best-effort; failure is non-fatal).\n  try {\n    await mkdir(join(opts.projectRoot, \".claude\", \".semantic-memory\"), { recursive: true });\n    await writeFile(cachePath, JSON.stringify({ ...result, ran_at_ms: start }, null, 2), \"utf-8\");\n  } catch {\n    // never let cache write block the result\n  }\n\n  return result;\n}\n\n/**\n * Surface filter — return findings with severity >= warn. Used by the SessionStart hook\n * to decide whether to emit anything at all.\n */\nexport function filterToDrift(result: HealthcheckResult): DriftFinding[] {\n  return result.findings.filter((f) => f.severity !== \"ok\");\n}\n\nfunction countBySeverity(findings: DriftFinding[]): { ok: number; warn: number; error: number } {\n  const counts = { ok: 0, warn: 0, error: 0 };\n  for (const f of findings) counts[f.severity]++;\n  return counts;\n}\n\nasync function runFastTier(opts: HealthcheckOptions): Promise<DriftFinding[]> {\n  const checks: Promise<DriftFinding | null>[] = [\n    checkPluginVersion(opts.projectRoot),\n    checkMcpJsonEntry(opts.projectRoot),\n    checkHookRegistration(opts.projectRoot),\n    checkHookDoubleRegistration(opts.projectRoot),\n    checkIndexFreshness(opts.projectRoot, opts.vaultPath),\n    checkSessionStaleness(opts.projectRoot),\n    checkAgentsContract(opts.projectRoot),\n    checkLegacyStateFiles(opts.projectRoot),\n    ...(await skillManifestChecks(opts.projectRoot)),\n  ];\n  const results = await Promise.all(checks.map((p) => p.catch((err) => failOpenWarn(err))));\n  return results.filter((r): r is DriftFinding => r !== null);\n}\n\nasync function runSlowTier(opts: HealthcheckOptions): Promise<DriftFinding[]> {\n  const findings: DriftFinding[] = [];\n  if (opts.vaultPath && existsSync(opts.vaultPath)) {\n    try {\n      const report = await lintVault(opts.vaultPath);\n      const total = report.findings.length;\n      if (total === 0) {\n        findings.push({ check: \"lint_vault\", severity: \"ok\", summary: `vault lint clean (${report.counts.filesLinted} files)` });\n      } else {\n        findings.push({\n          check: \"lint_vault\",\n          severity: report.counts.errors > 0 ? \"error\" : \"warn\",\n          summary: `vault lint: ${total} findings (errors=${report.counts.errors}, warnings=${report.counts.warnings})`,\n          detail: `Run \\`lint_vault\\` for the full report. Many lint findings need human review (stale notes, broken wikilinks).`,\n        });\n      }\n    } catch (err: any) {\n      findings.push({ check: \"lint_vault\", severity: \"warn\", summary: `lint_vault threw: ${err?.message ?? err}` });\n    }\n  }\n  return findings;\n}\n\nfunction failOpenWarn(err: unknown): DriftFinding {\n  return {\n    check: \"internal\",\n    severity: \"warn\",\n    summary: `healthcheck internal error: ${err instanceof Error ? err.message : String(err)}`,\n  };\n}\n\n// --- individual checks ---\n\nasync function checkPluginVersion(projectRoot: string): Promise<DriftFinding | null> {\n  const pkgPaths = [\n    join(projectRoot, \"node_modules\", \"@theglitchking\", \"semantic-memory\", \"package.json\"),\n    join(projectRoot, \"node_modules\", \"@theglitchking\", \"semantic-sidekick\", \"package.json\"),\n  ];\n  for (const p of pkgPaths) {\n    if (!existsSync(p)) continue;\n    try {\n      const installed = JSON.parse(await readFile(p, \"utf-8\"));\n      if (typeof installed?.version === \"string\") {\n        return { check: \"plugin_version\", severity: \"ok\", summary: `installed=${installed.version}` };\n      }\n    } catch {\n      // continue to next candidate\n    }\n  }\n  return null; // no installation present — not a drift event for non-npm dev environments\n}\n\nasync function checkMcpJsonEntry(projectRoot: string): Promise<DriftFinding | null> {\n  const mcpPath = join(projectRoot, \".mcp.json\");\n  if (!existsSync(mcpPath)) return null; // no .mcp.json — fine for dev\n  const data = JSON.parse(await readFile(mcpPath, \"utf-8\"));\n  const servers = data?.mcpServers ?? {};\n  const hasEntry = Object.keys(servers).some((k) => k === \"semantic-vault\" || k === \"semantic-sidekick\" || k === \"semantic-memory\");\n  if (!hasEntry) {\n    return {\n      check: \"mcp_json_entry\",\n      severity: \"warn\",\n      summary: \".mcp.json present but no semantic-memory/sidekick/vault server entry\",\n      fixable_via: \"mcp-reconcile\",\n    };\n  }\n  return { check: \"mcp_json_entry\", severity: \"ok\", summary: \".mcp.json server entry present\" };\n}\n\n// Events the plugin registers through its own hooks/hooks.json (resolved via\n// CLAUDE_PLUGIN_ROOT). On a plugin-style install these live in the plugin, not\n// the project's .claude/settings.json, so they must count as registered.\nfunction pluginRegisteredHookEvents(): string[] {\n  try {\n    const root = process.env.CLAUDE_PLUGIN_ROOT;\n    if (!root) return [];\n    const hooksPath = join(root, \"hooks\", \"hooks.json\");\n    if (!existsSync(hooksPath)) return [];\n    const data = JSON.parse(readFileSync(hooksPath, \"utf-8\"));\n    const hooks = data?.hooks ?? {};\n    return Object.keys(hooks).filter((e) => Array.isArray(hooks[e]) && hooks[e].length > 0);\n  } catch {\n    return [];\n  }\n}\n\nasync function checkHookRegistration(projectRoot: string): Promise<DriftFinding | null> {\n  const settings = join(projectRoot, \".claude\", \"settings.json\");\n  if (!existsSync(settings)) return null;\n  try {\n    const data = JSON.parse(await readFile(settings, \"utf-8\"));\n    const hooks = data?.hooks ?? {};\n    const required = [\"SessionStart\", \"UserPromptSubmit\", \"Stop\"];\n    const pluginEvents = pluginRegisteredHookEvents();\n    const missing: string[] = [];\n    for (const event of required) {\n      const arr = hooks[event];\n      const inSettings = Array.isArray(arr) && arr.length > 0;\n      if (!inSettings && !pluginEvents.includes(event)) missing.push(event);\n    }\n    if (missing.length > 0) {\n      return {\n        check: \"hook_registration\",\n        severity: \"warn\",\n        summary: `missing hook registrations: ${missing.join(\", \")}`,\n        detail: `Run \\`/relink\\` or reinstall the plugin to refresh hook registrations.`,\n      };\n    }\n    return { check: \"hook_registration\", severity: \"ok\", summary: \"all 3 hook events registered\" };\n  } catch (err: any) {\n    return failOpenWarn(err);\n  }\n}\n\n/**\n * Detect the double-registration that fires every hook twice: the SAME event\n * declared in BOTH the project's .claude/settings.json AND the plugin's own\n * hooks/hooks.json. On a plugin install the plugin already registers its hooks,\n * so a duplicate in settings.json makes vault-context.js (and friends) run twice —\n * e.g. the <vault-context> block injected twice per prompt.\n *\n * Only fires in a plugin context (CLAUDE_PLUGIN_ROOT present). npm-dependency\n * installs legitimately register via settings.json and have no plugin hooks.json,\n * so `pluginRegisteredHookEvents()` is empty and this is a silent no-op for them.\n */\nasync function checkHookDoubleRegistration(projectRoot: string): Promise<DriftFinding | null> {\n  const settings = join(projectRoot, \".claude\", \"settings.json\");\n  if (!existsSync(settings)) return null;\n  const pluginEvents = pluginRegisteredHookEvents();\n  if (pluginEvents.length === 0) return null; // not a plugin install / no plugin hooks to collide with\n  try {\n    const data = JSON.parse(await readFile(settings, \"utf-8\"));\n    const hooks = data?.hooks ?? {};\n    const doubled: string[] = [];\n    for (const event of [\"SessionStart\", \"UserPromptSubmit\", \"Stop\"]) {\n      const arr = hooks[event];\n      const inSettings = Array.isArray(arr) && arr.length > 0;\n      if (inSettings && pluginEvents.includes(event)) doubled.push(event);\n    }\n    if (doubled.length > 0) {\n      return {\n        check: \"hook_double_registration\",\n        severity: \"warn\",\n        summary: `hook event(s) registered in BOTH settings.json and the plugin — fires twice: ${doubled.join(\", \")}`,\n        detail:\n          `The plugin's hooks/hooks.json already registers ${doubled.join(\", \")}, so the duplicate ` +\n          `registration in .claude/settings.json makes each hook run twice (e.g. the <vault-context> ` +\n          `block injected twice per prompt). Remove the \"hooks\" block from .claude/settings.json — the ` +\n          `plugin's hooks.json is the single source of truth for plugin installs.`,\n        fixable_via: \"none\",\n      };\n    }\n    return { check: \"hook_double_registration\", severity: \"ok\", summary: \"no double-registered hooks\" };\n  } catch (err: any) {\n    return failOpenWarn(err);\n  }\n}\n\nasync function checkIndexFreshness(projectRoot: string, vaultPath?: string): Promise<DriftFinding | null> {\n  const vault = vaultPath ?? defaultVaultPath(projectRoot);\n  if (!vault || !existsSync(vault)) return null;\n  const indexDir = join(vault, \".semantic-sidekick-index\");\n  const meta = join(indexDir, \"meta.json\");\n  if (!existsSync(meta)) {\n    return {\n      check: \"index_freshness\",\n      severity: \"warn\",\n      summary: \"no index built yet\",\n      detail: \"Run `reindex` to build the vector index.\",\n      fixable_via: \"reindex\",\n    };\n  }\n  try {\n    const data = JSON.parse(await readFile(meta, \"utf-8\"));\n    if (typeof data.indexedAt === \"string\") {\n      return { check: \"index_freshness\", severity: \"ok\", summary: `last reindex ${data.indexedAt}` };\n    }\n  } catch {\n    // ignore\n  }\n  return null;\n}\n\nasync function checkSessionStaleness(projectRoot: string): Promise<DriftFinding | null> {\n  const sessionPath = join(projectRoot, \".claude\", \".semantic-memory\", \"session.json\");\n  if (!existsSync(sessionPath)) return null;\n  try {\n    const state = JSON.parse(await readFile(sessionPath, \"utf-8\"));\n    if (state?.closed_at) return null;\n    const last = state?.last_activity_at;\n    if (typeof last !== \"string\") return null;\n    const ageMs = Date.now() - new Date(last).getTime();\n    if (ageMs > 24 * 60 * 60 * 1000) {\n      return {\n        check: \"session_staleness\",\n        severity: \"warn\",\n        summary: `session ${state.id} stale (>${Math.round(ageMs / (60 * 60 * 1000))}h since activity)`,\n        detail: `Either resume the session (run session_run / session_finish) or remove .claude/.semantic-memory/session.json to abandon it.`,\n      };\n    }\n    return { check: \"session_staleness\", severity: \"ok\", summary: `session ${state.id} active` };\n  } catch {\n    return null;\n  }\n}\n\nasync function checkLegacyStateFiles(projectRoot: string): Promise<DriftFinding | null> {\n  // Detect v1.1-and-earlier state files at .claude/.sidekick-*. v1.2 moved these to\n  // .claude/.semantic-memory/. The hook still reads them via fallback for backwards-\n  // compat, but they should be migrated explicitly so the legacy paths stop existing.\n  const legacy = [\n    \".sidekick-mode\",\n    \".sidekick-fingerprints.json\",\n    \".sidekick-capture-pending.json\",\n  ];\n  const present: string[] = [];\n  for (const name of legacy) {\n    if (existsSync(join(projectRoot, \".claude\", name))) {\n      present.push(name);\n    }\n  }\n  if (present.length === 0) {\n    return { check: \"legacy_state_files\", severity: \"ok\", summary: \"no legacy state files\" };\n  }\n  return {\n    check: \"legacy_state_files\",\n    severity: \"warn\",\n    summary: `${present.length} legacy state file${present.length === 1 ? \"\" : \"s\"} at .claude/.sidekick-*`,\n    detail:\n      `Files: ${present.join(\", \")}. Run \\`bin/semantic-memory migrate-state\\` to move them under .claude/.semantic-memory/. ` +\n      `These files are still being read for backwards-compat through v1.x; the legacy fallback is removed in v2.0.`,\n    fixable_via: \"state-migrate\",\n  };\n}\n\nasync function checkAgentsContract(projectRoot: string): Promise<DriftFinding | null> {\n  const path = join(projectRoot, \"AGENTS.md\");\n  if (!existsSync(path)) return null; // optional artifact\n  try {\n    const raw = await readFile(path, \"utf-8\");\n    const begin = raw.indexOf(\"<!-- semantic-memory:begin contract -->\");\n    const end = raw.indexOf(\"<!-- semantic-memory:end contract -->\");\n    if (begin === -1 || end === -1) {\n      return {\n        check: \"agents_contract\",\n        severity: \"warn\",\n        summary: \"AGENTS.md exists but lacks managed-block markers\",\n        detail: \"Either move custom content to a Local Notes section, or delete AGENTS.md and run `regenerate_contract` to bootstrap.\",\n        fixable_via: \"regenerate-contract\",\n      };\n    }\n    return { check: \"agents_contract\", severity: \"ok\", summary: \"AGENTS.md managed block intact\" };\n  } catch {\n    return null;\n  }\n}\n\nasync function skillManifestChecks(projectRoot: string): Promise<Promise<DriftFinding | null>[]> {\n  const home = homedir();\n  const targets = [\n    { agent: \"claude\", path: join(home, \".claude\", \"skills\") },\n    { agent: \"codex\", path: join(home, \".codex\", \"skills\") },\n    { agent: \"copilot\", path: join(home, \".copilot\", \"skills\") },\n    { agent: \"pi\", path: join(home, \".pi\", \"agent\", \"skills\") },\n    { agent: \"claude-local\", path: join(projectRoot, \".claude\", \"skills\") },\n  ];\n  const out: Promise<DriftFinding | null>[] = [];\n  for (const t of targets) {\n    out.push(checkOneSkillManifest(t.agent, t.path));\n  }\n  return out;\n}\n\nasync function checkOneSkillManifest(agentLabel: string, skillsRoot: string): Promise<DriftFinding | null> {\n  const manifestPath = join(skillsRoot, \".semantic-memory-skill-manifest.json\");\n  if (!existsSync(manifestPath)) return null; // not installed for this agent — fine\n  try {\n    const raw = await readFile(manifestPath, \"utf-8\");\n    const manifest = JSON.parse(raw);\n    if (typeof manifest?.installed_at !== \"string\") return null;\n    const age = Date.now() - new Date(manifest.installed_at).getTime();\n    // Manifest itself is the source of truth; deeper sha-recheck happens via slow tier\n    return {\n      check: `skill_manifest:${agentLabel}`,\n      severity: \"ok\",\n      summary: `${agentLabel} skills installed v${manifest.version} (${Math.round(age / (24 * 60 * 60 * 1000))}d ago)`,\n    };\n  } catch {\n    return null;\n  }\n}\n\nfunction defaultVaultPath(projectRoot: string): string {\n  return join(projectRoot, \".claude\", \".vault\");\n}\n\n/**\n * Format a drift summary for the SessionStart hook. 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package/dist/chunk-5ZKNO6ZD.js

@@ -0,0 +1,96 @@
+// src/core/decay.ts
+import { existsSync, readFileSync } from "fs";
+import { join } from "path";
+import { parse as parseYaml } from "yaml";
+function normalizeVerifiedDate(v) {
+  if (typeof v === "string") return v;
+  if (v instanceof Date && !Number.isNaN(v.getTime())) return v.toISOString();
+  return void 0;
+}
+var DEFAULT_DECAY_CONFIG = {
+  enabled: true,
+  default_half_life_days: 365,
+  per_type: {
+    decision: 365,
+    note: 365,
+    gotcha: 180,
+    source: null,
+    // never decays
+    proposal: 14
+  },
+  floor: 0.1,
+  hotness_boost: { enabled: false, cap: 2 }
+};
+var MS_PER_DAY = 24 * 60 * 60 * 1e3;
+var EVERGREEN_MAX_AGE_DAYS = 365;
+function fresh(reason, ageDays = 0, halfLife = 0, evergreen) {
+  return { multiplier: 1, age_days: ageDays, effective_half_life: halfLife, reason, evergreen };
+}
+function computeDecay(input) {
+  const { config } = input;
+  if (!config.enabled) return fresh("decay disabled");
+  let halfLife = config.default_half_life_days;
+  if (input.type && Object.prototype.hasOwnProperty.call(config.per_type, input.type)) {
+    const perType = config.per_type[input.type];
+    if (perType === null) {
+      return fresh(`type=${input.type} never decays`, ageDaysOf(input), Infinity);
+    }
+    if (typeof perType === "number" && perType > 0) halfLife = perType;
+  }
+  if (!input.last_verified) return fresh("no last_verified (fail open)", 0, halfLife);
+  const lastMs = Date.parse(input.last_verified);
+  if (Number.isNaN(lastMs)) return fresh("unparseable last_verified (fail open)", 0, halfLife);
+  const now = input.nowMs ?? Date.now();
+  const ageDays = (now - lastMs) / MS_PER_DAY;
+  if (ageDays <= 0) return fresh("last_verified in the future (fail open)", ageDays, halfLife);
+  if (input.evergreen && ageDays < EVERGREEN_MAX_AGE_DAYS) {
+    return fresh("evergreen (verified within 365d)", ageDays, halfLife, true);
+  }
+  let effHalfLife = halfLife;
+  if (config.hotness_boost.enabled && input.inbound_link_count && input.inbound_link_count > 0) {
+    const boost = Math.min(input.inbound_link_count / 5, config.hotness_boost.cap - 1);
+    effHalfLife = halfLife * (1 + Math.max(boost, 0));
+  }
+  const raw = Math.pow(0.5, ageDays / effHalfLife);
+  const multiplier = Math.max(raw, config.floor);
+  return {
+    multiplier,
+    age_days: ageDays,
+    effective_half_life: effHalfLife,
+    reason: `type=${input.type ?? "default"}`,
+    evergreen: input.evergreen
+  };
+}
+function ageDaysOf(input) {
+  if (!input.last_verified) return 0;
+  const lastMs = Date.parse(input.last_verified);
+  if (Number.isNaN(lastMs)) return 0;
+  const now = input.nowMs ?? Date.now();
+  return Math.max((now - lastMs) / MS_PER_DAY, 0);
+}
+function loadDecayConfig(vaultPath) {
+  try {
+    const schemaPath = join(vaultPath, "vault.schema.yml");
+    if (!existsSync(schemaPath)) return DEFAULT_DECAY_CONFIG;
+    const parsed = parseYaml(readFileSync(schemaPath, "utf-8"));
+    const d = parsed?.decay;
+    if (!d || typeof d !== "object") return DEFAULT_DECAY_CONFIG;
+    return {
+      enabled: typeof d.enabled === "boolean" ? d.enabled : DEFAULT_DECAY_CONFIG.enabled,
+      default_half_life_days: typeof d.default_half_life_days === "number" ? d.default_half_life_days : DEFAULT_DECAY_CONFIG.default_half_life_days,
+      per_type: { ...DEFAULT_DECAY_CONFIG.per_type, ...d.per_type ?? {} },
+      floor: typeof d.floor === "number" ? d.floor : DEFAULT_DECAY_CONFIG.floor,
+      hotness_boost: { ...DEFAULT_DECAY_CONFIG.hotness_boost, ...d.hotness_boost ?? {} }
+    };
+  } catch {
+    return DEFAULT_DECAY_CONFIG;
+  }
+}
+
+export {
+  normalizeVerifiedDate,
+  DEFAULT_DECAY_CONFIG,
+  computeDecay,
+  loadDecayConfig
+};
+//# sourceMappingURL=chunk-5ZKNO6ZD.js.map

package/dist/chunk-5ZKNO6ZD.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/core/decay.ts"],"sourcesContent":["import { existsSync, readFileSync } from \"node:fs\";\nimport { join } from \"node:path\";\nimport { parse as parseYaml } from \"yaml\";\n\n/**\n * Confidence decay (v1.3).\n *\n * Pure, side-effect-free ranking signal: a note's relevance decays smoothly with\n * the time since it was last *verified* (not merely edited). Load-bearing notes\n * resist decay (longer half-life), source notes never decay, evergreen notes are\n * pinned until their evergreen claim itself expires, and an explicit re-verify\n * resets the clock.\n *\n * The multiplier composes MULTIPLICATIVELY with the existing priority/confidence\n * signals at search time — it never replaces them. Floored so notes down-weight\n * but never disappear.\n */\n\nexport interface DecayConfig {\n  enabled: boolean;\n  default_half_life_days: number;\n  /** Per-type half-life in days. `null` means \"never decays\" (e.g. source notes). */\n  per_type: Partial<Record<string, number | null>>;\n  floor: number;\n  hotness_boost: { enabled: boolean; cap: number };\n}\n\nexport interface DecayInput {\n  type?: string;\n  last_verified?: string;\n  evergreen?: boolean;\n  inbound_link_count?: number;\n  config: DecayConfig;\n  /** Override \"now\" — used by tests. */\n  nowMs?: number;\n}\n\nexport interface DecayResult {\n  multiplier: number;\n  age_days: number;\n  effective_half_life: number;\n  reason: string;\n  evergreen?: boolean;\n}\n\n/**\n * Normalize a frontmatter `last_verified` value to an ISO string. YAML parses an\n * unquoted `last_verified: 2019-01-01` into a Date, not a string, so a bare\n * `typeof === \"string\"` check would silently drop it and disable decay. Accepts\n * string or Date; anything else → undefined (fail open).\n */\nexport function normalizeVerifiedDate(v: unknown): string | undefined {\n  if (typeof v === \"string\") return v;\n  if (v instanceof Date && !Number.isNaN(v.getTime())) return v.toISOString();\n  return undefined;\n}\n\n/** The default decay config, mirrored in the default vault schema YAML. */\nexport const DEFAULT_DECAY_CONFIG: DecayConfig = {\n  enabled: true,\n  default_half_life_days: 365,\n  per_type: {\n    decision: 365,\n    note: 365,\n    gotcha: 180,\n    source: null, // never decays\n    proposal: 14,\n  },\n  floor: 0.1,\n  hotness_boost: { enabled: false, cap: 2.0 },\n};\n\nconst MS_PER_DAY = 24 * 60 * 60 * 1000;\nconst EVERGREEN_MAX_AGE_DAYS = 365;\n\nfunction fresh(reason: string, ageDays = 0, halfLife = 0, evergreen?: boolean): DecayResult {\n  return { multiplier: 1.0, age_days: ageDays, effective_half_life: halfLife, reason, evergreen };\n}\n\n/**\n * Compute the decay multiplier for one note. Fails open (multiplier 1.0) on any\n * uncertainty — disabled config, missing/invalid/future last_verified — so decay\n * can only ever DOWN-rank a note we're confident is old, never penalize ambiguity.\n */\nexport function computeDecay(input: DecayInput): DecayResult {\n  const { config } = input;\n  if (!config.enabled) return fresh(\"decay disabled\");\n\n  // Resolve half-life. A `null` per-type entry means this type never decays.\n  let halfLife = config.default_half_life_days;\n  if (input.type && Object.prototype.hasOwnProperty.call(config.per_type, input.type)) {\n    const perType = config.per_type[input.type];\n    if (perType === null) {\n      return fresh(`type=${input.type} never decays`, ageDaysOf(input), Infinity);\n    }\n    if (typeof perType === \"number\" && perType > 0) halfLife = perType;\n  }\n\n  // Age since last verification. Missing/invalid/future → fail open.\n  if (!input.last_verified) return fresh(\"no last_verified (fail open)\", 0, halfLife);\n  const lastMs = Date.parse(input.last_verified);\n  if (Number.isNaN(lastMs)) return fresh(\"unparseable last_verified (fail open)\", 0, halfLife);\n  const now = input.nowMs ?? Date.now();\n  const ageDays = (now - lastMs) / MS_PER_DAY;\n  if (ageDays <= 0) return fresh(\"last_verified in the future (fail open)\", ageDays, halfLife);\n\n  // Evergreen: pinned at 1.0 while its verification is fresh; falls through to\n  // normal decay once the evergreen claim is older than a year (forces re-affirmation).\n  if (input.evergreen && ageDays < EVERGREEN_MAX_AGE_DAYS) {\n    return fresh(\"evergreen (verified within 365d)\", ageDays, halfLife, true);\n  }\n\n  // Backlink hotness (Phase 7 — feature-flagged off by default): a heavily-linked\n  // note is likely load-bearing, so extend its effective half-life.\n  let effHalfLife = halfLife;\n  if (config.hotness_boost.enabled && input.inbound_link_count && input.inbound_link_count > 0) {\n    const boost = Math.min(input.inbound_link_count / 5, config.hotness_boost.cap - 1);\n    effHalfLife = halfLife * (1 + Math.max(boost, 0));\n  }\n\n  const raw = Math.pow(0.5, ageDays / effHalfLife);\n  const multiplier = Math.max(raw, config.floor);\n  return {\n    multiplier,\n    age_days: ageDays,\n    effective_half_life: effHalfLife,\n    reason: `type=${input.type ?? \"default\"}`,\n    evergreen: input.evergreen,\n  };\n}\n\nfunction ageDaysOf(input: DecayInput): number {\n  if (!input.last_verified) return 0;\n  const lastMs = Date.parse(input.last_verified);\n  if (Number.isNaN(lastMs)) return 0;\n  const now = input.nowMs ?? Date.now();\n  return Math.max((now - lastMs) / MS_PER_DAY, 0);\n}\n\n/**\n * Load the decay config from a vault's `vault.schema.yml` `decay:` block, merged\n * over the shipped defaults. Missing file / block / parse error → defaults.\n * Synchronous + memoization-friendly (callers cache the result).\n */\nexport function loadDecayConfig(vaultPath: string): DecayConfig {\n  try {\n    const schemaPath = join(vaultPath, \"vault.schema.yml\");\n    if (!existsSync(schemaPath)) return DEFAULT_DECAY_CONFIG;\n    const parsed = parseYaml(readFileSync(schemaPath, \"utf-8\")) as { decay?: Partial<DecayConfig> } | null;\n    const d = parsed?.decay;\n    if (!d || typeof d !== \"object\") return DEFAULT_DECAY_CONFIG;\n    return {\n      enabled: typeof d.enabled === \"boolean\" ? d.enabled : DEFAULT_DECAY_CONFIG.enabled,\n      default_half_life_days:\n        typeof d.default_half_life_days === \"number\" ? d.default_half_life_days : DEFAULT_DECAY_CONFIG.default_half_life_days,\n      per_type: { ...DEFAULT_DECAY_CONFIG.per_type, ...(d.per_type ?? {}) },\n      floor: typeof d.floor === \"number\" ? d.floor : DEFAULT_DECAY_CONFIG.floor,\n      hotness_boost: { ...DEFAULT_DECAY_CONFIG.hotness_boost, ...(d.hotness_boost ?? {}) },\n    };\n  } catch {\n    return DEFAULT_DECAY_CONFIG;\n  }\n}\n"],"mappings":";AAAA,SAAS,YAAY,oBAAoB;AACzC,SAAS,YAAY;AACrB,SAAS,SAAS,iBAAiB;AAiD5B,SAAS,sBAAsB,GAAgC;AACpE,MAAI,OAAO,MAAM,SAAU,QAAO;AAClC,MAAI,aAAa,QAAQ,CAAC,OAAO,MAAM,EAAE,QAAQ,CAAC,EAAG,QAAO,EAAE,YAAY;AAC1E,SAAO;AACT;AAGO,IAAM,uBAAoC;AAAA,EAC/C,SAAS;AAAA,EACT,wBAAwB;AAAA,EACxB,UAAU;AAAA,IACR,UAAU;AAAA,IACV,MAAM;AAAA,IACN,QAAQ;AAAA,IACR,QAAQ;AAAA;AAAA,IACR,UAAU;AAAA,EACZ;AAAA,EACA,OAAO;AAAA,EACP,eAAe,EAAE,SAAS,OAAO,KAAK,EAAI;AAC5C;AAEA,IAAM,aAAa,KAAK,KAAK,KAAK;AAClC,IAAM,yBAAyB;AAE/B,SAAS,MAAM,QAAgB,UAAU,GAAG,WAAW,GAAG,WAAkC;AAC1F,SAAO,EAAE,YAAY,GAAK,UAAU,SAAS,qBAAqB,UAAU,QAAQ,UAAU;AAChG;AAOO,SAAS,aAAa,OAAgC;AAC3D,QAAM,EAAE,OAAO,IAAI;AACnB,MAAI,CAAC,OAAO,QAAS,QAAO,MAAM,gBAAgB;AAGlD,MAAI,WAAW,OAAO;AACtB,MAAI,MAAM,QAAQ,OAAO,UAAU,eAAe,KAAK,OAAO,UAAU,MAAM,IAAI,GAAG;AACnF,UAAM,UAAU,OAAO,SAAS,MAAM,IAAI;AAC1C,QAAI,YAAY,MAAM;AACpB,aAAO,MAAM,QAAQ,MAAM,IAAI,iBAAiB,UAAU,KAAK,GAAG,QAAQ;AAAA,IAC5E;AACA,QAAI,OAAO,YAAY,YAAY,UAAU,EAAG,YAAW;AAAA,EAC7D;AAGA,MAAI,CAAC,MAAM,cAAe,QAAO,MAAM,gCAAgC,GAAG,QAAQ;AAClF,QAAM,SAAS,KAAK,MAAM,MAAM,aAAa;AAC7C,MAAI,OAAO,MAAM,MAAM,EAAG,QAAO,MAAM,yCAAyC,GAAG,QAAQ;AAC3F,QAAM,MAAM,MAAM,SAAS,KAAK,IAAI;AACpC,QAAM,WAAW,MAAM,UAAU;AACjC,MAAI,WAAW,EAAG,QAAO,MAAM,2CAA2C,SAAS,QAAQ;AAI3F,MAAI,MAAM,aAAa,UAAU,wBAAwB;AACvD,WAAO,MAAM,oCAAoC,SAAS,UAAU,IAAI;AAAA,EAC1E;AAIA,MAAI,cAAc;AAClB,MAAI,OAAO,cAAc,WAAW,MAAM,sBAAsB,MAAM,qBAAqB,GAAG;AAC5F,UAAM,QAAQ,KAAK,IAAI,MAAM,qBAAqB,GAAG,OAAO,cAAc,MAAM,CAAC;AACjF,kBAAc,YAAY,IAAI,KAAK,IAAI,OAAO,CAAC;AAAA,EACjD;AAEA,QAAM,MAAM,KAAK,IAAI,KAAK,UAAU,WAAW;AAC/C,QAAM,aAAa,KAAK,IAAI,KAAK,OAAO,KAAK;AAC7C,SAAO;AAAA,IACL;AAAA,IACA,UAAU;AAAA,IACV,qBAAqB;AAAA,IACrB,QAAQ,QAAQ,MAAM,QAAQ,SAAS;AAAA,IACvC,WAAW,MAAM;AAAA,EACnB;AACF;AAEA,SAAS,UAAU,OAA2B;AAC5C,MAAI,CAAC,MAAM,cAAe,QAAO;AACjC,QAAM,SAAS,KAAK,MAAM,MAAM,aAAa;AAC7C,MAAI,OAAO,MAAM,MAAM,EAAG,QAAO;AACjC,QAAM,MAAM,MAAM,SAAS,KAAK,IAAI;AACpC,SAAO,KAAK,KAAK,MAAM,UAAU,YAAY,CAAC;AAChD;AAOO,SAAS,gBAAgB,WAAgC;AAC9D,MAAI;AACF,UAAM,aAAa,KAAK,WAAW,kBAAkB;AACrD,QAAI,CAAC,WAAW,UAAU,EAAG,QAAO;AACpC,UAAM,SAAS,UAAU,aAAa,YAAY,OAAO,CAAC;AAC1D,UAAM,IAAI,QAAQ;AAClB,QAAI,CAAC,KAAK,OAAO,MAAM,SAAU,QAAO;AACxC,WAAO;AAAA,MACL,SAAS,OAAO,EAAE,YAAY,YAAY,EAAE,UAAU,qBAAqB;AAAA,MAC3E,wBACE,OAAO,EAAE,2BAA2B,WAAW,EAAE,yBAAyB,qBAAqB;AAAA,MACjG,UAAU,EAAE,GAAG,qBAAqB,UAAU,GAAI,EAAE,YAAY,CAAC,EAAG;AAAA,MACpE,OAAO,OAAO,EAAE,UAAU,WAAW,EAAE,QAAQ,qBAAqB;AAAA,MACpE,eAAe,EAAE,GAAG,qBAAqB,eAAe,GAAI,EAAE,iBAAiB,CAAC,EAAG;AAAA,IACrF;AAAA,EACF,QAAQ;AACN,WAAO;AAAA,EACT;AACF;","names":[]}