gsd-pi 2.81.0-dev.72a81bdf3 → 2.82.0-dev.20138ae42

package/dist/resources/extensions/gsd/context-store.js

@@ -47,6 +47,118 @@ export function queryDecisions(opts) {
         return [];
     }
 }
+/**
+ * Internal: shared core for the two memory-sourced decision queries. Reads
+ * memory rows tagged with `sourceDecisionId` and reconstructs `Decision[]`
+ * from their `structured_fields` JSON.
+ *
+ * @param includeSuperseded — when false, drops rows whose
+ *   `structured_fields.superseded_by` is non-null. The supersedes-chain is
+ *   captured by the backfill (`memory-backfill.ts`) and kept in sync by
+ *   the backfill's drift auto-heal pass.
+ */
+function readDecisionsFromMemories(opts, includeSuperseded) {
+    if (!isDbAvailable())
+        return [];
+    const adapter = _getAdapter();
+    if (!adapter)
+        return [];
+    try {
+        const clauses = [
+            "category = 'architecture'",
+            "structured_fields LIKE '%\"sourceDecisionId\":\"%'",
+        ];
+        const params = {};
+        if (opts?.milestoneId) {
+            // when_context is a free-text JSON value; substring match preserves the
+            // semantics of `when_context LIKE '%milestoneId%'` on the legacy table.
+            clauses.push("json_extract(structured_fields, '$.when_context') LIKE :milestone_pattern");
+            params[':milestone_pattern'] = `%${opts.milestoneId}%`;
+        }
+        if (opts?.scope) {
+            // Stage 1 used `json_extract` in main (post-merge); preserve that
+            // style here. Exact equality on the JSON value avoids the prefix
+            // collision risk LIKE patterns had (scope=M001 vs scope=M001-S01).
+            clauses.push("json_extract(structured_fields, '$.scope') = :scope");
+            params[':scope'] = opts.scope;
+        }
+        const sql = `SELECT seq, structured_fields FROM memories WHERE ${clauses.join(' AND ')} ORDER BY seq`;
+        const rows = adapter.prepare(sql).all(params);
+        const decisions = [];
+        for (const row of rows) {
+            const seq = row['seq'];
+            const sfRaw = row['structured_fields'];
+            if (!sfRaw)
+                continue;
+            let sf;
+            try {
+                sf = JSON.parse(sfRaw);
+            }
+            catch {
+                continue;
+            }
+            const sourceId = sf['sourceDecisionId'];
+            if (typeof sourceId !== 'string' || sourceId.length === 0)
+                continue;
+            // Decision-level superseded status lives in structured_fields.superseded_by
+            // (written by mirrorDecisionToMemory / memory-backfill.ts). The top-level
+            // memories.superseded_by column is intentionally never set for decision mirrors,
+            // so active-only filtering must be done here in the JS loop.
+            const supersededBy = typeof sf['superseded_by'] === 'string' ? sf['superseded_by'] : null;
+            if (!includeSuperseded && supersededBy)
+                continue;
+            decisions.push({
+                seq,
+                id: sourceId,
+                when_context: typeof sf['when_context'] === 'string' ? sf['when_context'] : '',
+                scope: typeof sf['scope'] === 'string' ? sf['scope'] : '',
+                decision: typeof sf['decision'] === 'string' ? sf['decision'] : '',
+                choice: typeof sf['choice'] === 'string' ? sf['choice'] : '',
+                rationale: typeof sf['rationale'] === 'string' ? sf['rationale'] : '',
+                revisable: typeof sf['revisable'] === 'string' ? sf['revisable'] : '',
+                made_by: (typeof sf['made_by'] === 'string' ? sf['made_by'] : 'agent'),
+                superseded_by: supersededBy,
+            });
+        }
+        return decisions;
+    }
+    catch {
+        return [];
+    }
+}
+/**
+ * ADR-013 Phase 6 cutover (Stage 1): read **active** decisions from the
+ * `memories` table instead of the legacy `decisions` table. Returns the
+ * same `Decision[]` shape as `queryDecisions` so downstream formatters
+ * work unchanged.
+ *
+ * Filter semantics match `queryDecisions` exactly:
+ * - active only (skips rows where `structured_fields.superseded_by` is set)
+ * - `milestoneId`: substring match on `structured_fields.when_context`
+ * - `scope`: exact match on `structured_fields.scope`
+ *
+ * Used by the prompt-inline path (`inlineDecisionsFromDb` in
+ * `auto-prompts.ts`). For the projection regen (which renders superseded
+ * rows too), see `getAllDecisionsFromMemories`.
+ */
+export function queryDecisionsFromMemories(opts) {
+    return readDecisionsFromMemories(opts, /* includeSuperseded */ false);
+}
+/**
+ * ADR-013 Phase 6 cutover (Stage 2a): read **all** decisions (active +
+ * superseded) from the `memories` table. Used by the DECISIONS.md
+ * projection regen in `saveDecisionToDb`, which must render the full
+ * supersedes-chain for the canonical register format.
+ *
+ * Equivalent to `SELECT * FROM decisions ORDER BY seq` over the legacy
+ * table — but sourced from memories so the legacy table can be retired
+ * in Stage 3. Includes `superseded_by` reconstructed from
+ * `structured_fields.superseded_by` (populated by the backfill's drift
+ * auto-heal pass).
+ */
+export function getAllDecisionsFromMemories() {
+    return readDecisionsFromMemories(undefined, /* includeSuperseded */ true);
+}
 /**
  * Query active (non-superseded) requirements with optional filters.
  * - milestoneId: combined with sliceId for precise filtering (e.g. %M005/S01%)

package/dist/resources/extensions/gsd/crash-recovery.js

@@ -23,7 +23,8 @@
 import { emitJournalEvent, queryJournal, } from "./journal.js";
 import { readFileSync, unlinkSync, existsSync } from "node:fs";
 import { join } from "node:path";
-import { findStaleWorkerForProject, getAllAutoWorkers, } from "./db/auto-workers.js";
+import { findStaleWorkerForProject, getAllAutoWorkers, markWorkerCrashed, } from "./db/auto-workers.js";
+import { markLatestActiveForWorkerCanceled } from "./db/unit-dispatches.js";
 import { getRuntimeKv, setRuntimeKv, deleteRuntimeKv } from "./db/runtime-kv.js";
 import { _getAdapter, isDbAvailable } from "./gsd-db.js";
 import { gsdRoot, normalizeRealPath } from "./paths.js";
@@ -34,6 +35,16 @@ const SESSION_FILE_KV_KEY = "session_file";
 function lockPath(basePath) {
     return join(gsdRoot(basePath), effectiveLockFile());
 }
+function clearLegacyLockFile(basePath) {
+    try {
+        const p = lockPath(basePath);
+        if (existsSync(p))
+            unlinkSync(p);
+    }
+    catch {
+        // Best-effort.
+    }
+}
 function readLegacyLock(basePath) {
     try {
         const p = lockPath(basePath);
@@ -166,21 +177,36 @@ export function writeLock(basePath, unitType, unitId, sessionFile) {
  * stale session-file pointer.
  */
 export function clearLock(basePath) {
+    clearLegacyLockFile(basePath);
+    if (!isDbAvailable())
+        return;
     try {
-        const p = lockPath(basePath);
-        if (existsSync(p))
-            unlinkSync(p);
+        const projectRoot = normalizeRealPath(basePath);
+        const worker = findActiveWorkerForCurrentProcess(projectRoot);
+        if (!worker)
+            return;
+        deleteRuntimeKv("worker", worker.worker_id, SESSION_FILE_KV_KEY);
     }
     catch {
         // Best-effort.
     }
+}
+/**
+ * Clear a stale DB-backed worker lock after readCrashLock/findStaleWorkerForProject
+ * has identified a dead worker. Unlike clearLock(), this targets the stale
+ * worker row instead of the current process's active worker.
+ */
+export function clearStaleWorkerLock(basePath) {
+    clearLegacyLockFile(basePath);
     if (!isDbAvailable())
         return;
     try {
         const projectRoot = normalizeRealPath(basePath);
-        const worker = findActiveWorkerForCurrentProcess(projectRoot);
+        const worker = findStaleWorkerForProject(projectRoot);
         if (!worker)
             return;
+        markLatestActiveForWorkerCanceled(worker.worker_id, "crash-recovered");
+        markWorkerCrashed(worker.worker_id);
         deleteRuntimeKv("worker", worker.worker_id, SESSION_FILE_KV_KEY);
     }
     catch {

package/dist/resources/extensions/gsd/db/unit-dispatches.js

@@ -391,16 +391,17 @@ export function getRecentUnitKeysForProjectRoot(projectRootRealpath, limit = 20)
     if (!isDbAvailable())
         return [];
     const db = _getAdapter();
-    const rows = db.prepare(`SELECT ud.unit_id
+    const rows = db.prepare(`SELECT ud.unit_type, ud.unit_id
      FROM unit_dispatches ud
      INNER JOIN workers w ON w.worker_id = ud.worker_id
      WHERE w.project_root_realpath = :project_root_realpath
+       AND w.status != 'crashed'
      ORDER BY ud.started_at DESC, ud.id DESC
      LIMIT :limit`).all({
         ":project_root_realpath": projectRootRealpath,
         ":limit": limit,
     });
-    return rows.reverse().map((r) => ({ key: r.unit_id }));
+    return rows.reverse().map((r) => ({ key: `${r.unit_type}/${r.unit_id}` }));
 }
 /**
  * Fetch dispatches for a milestone filtered by status. Useful for janitors

package/dist/resources/extensions/gsd/db-writer.js

@@ -210,16 +210,62 @@ export async function nextDecisionId() {
         return 'D001';
     }
 }
-/** Synchronous variant for use inside db.transaction(). */
-function nextDecisionIdSync(adapter) {
+/**
+ * ADR-013 Stage 3: compute the next `D###` identifier across both the legacy
+ * `decisions` table AND the `memories.structured_fields.sourceDecisionId`
+ * surface. Returns the max numeric suffix from either side + 1, three-digit
+ * padded.
+ *
+ * Used by `saveDecisionToDb` once writes to the `decisions` table stop —
+ * new decisions live only in memories, but historical IDs sit in both
+ * places during the cutover bake. The cross-surface max keeps IDs
+ * monotonic and avoids collisions on the next save.
+ */
+function nextDecisionIdAcrossSurfaces(adapter) {
     if (!adapter)
         return 'D001';
-    const row = adapter
-        .prepare('SELECT MAX(CAST(SUBSTR(id, 2) AS INTEGER)) as max_num FROM decisions')
-        .get();
-    const maxNum = row ? row['max_num'] : null;
-    if (maxNum == null || isNaN(maxNum))
-        return 'D001';
+    let maxNum = 0;
+    // Legacy table — best-effort.
+    try {
+        const row = adapter
+            .prepare('SELECT MAX(CAST(SUBSTR(id, 2) AS INTEGER)) as max_num FROM decisions')
+            .get();
+        const candidate = row ? row['max_num'] : null;
+        if (typeof candidate === 'number' && Number.isFinite(candidate)) {
+            maxNum = Math.max(maxNum, candidate);
+        }
+    }
+    catch {
+        // fall through to memory-only
+    }
+    // Memory surface: scan structuredFields.sourceDecisionId for D### values.
+    // SQLite LIKE on the JSON-stringified field is sufficient — rows tagged
+    // with sourceDecisionId are bounded by the decisions count.
+    try {
+        const rows = adapter
+            .prepare("SELECT structured_fields FROM memories WHERE structured_fields LIKE '%\"sourceDecisionId\":\"D%'")
+            .all();
+        for (const row of rows) {
+            if (!row.structured_fields)
+                continue;
+            let sf;
+            try {
+                sf = JSON.parse(row.structured_fields);
+            }
+            catch {
+                continue;
+            }
+            const sourceId = sf['sourceDecisionId'];
+            if (typeof sourceId !== 'string' || !sourceId.startsWith('D'))
+                continue;
+            const num = parseInt(sourceId.slice(1), 10);
+            if (Number.isFinite(num) && num > maxNum)
+                maxNum = num;
+        }
+    }
+    catch {
+        // best-effort
+    }
     const next = maxNum + 1;
     return `D${String(next).padStart(3, '0')}`;
 }
@@ -376,38 +422,55 @@ export async function saveDecisionToDb(fields, basePath) {
     try {
         const db = await import('./gsd-db.js');
         const adapter = db._getAdapter();
-        const id = db.transaction(() => {
-            const nextId = nextDecisionIdSync(adapter);
-            db.upsertDecision({
-                id: nextId,
-                when_context: fields.when_context ?? '',
-                scope: fields.scope,
-                decision: fields.decision,
-                choice: fields.choice,
-                rationale: fields.rationale,
-                revisable: fields.revisable ?? 'Yes',
-                made_by: fields.made_by ?? 'agent',
-                source: fields.source ?? 'discussion',
-                superseded_by: null,
+        const normalized = {
+            ...fields,
+            when_context: fields.when_context ?? '',
+            revisable: fields.revisable ?? 'Yes',
+            made_by: fields.made_by ?? 'agent',
+            source: fields.source ?? 'discussion',
+        };
+        // ADR-013 Stage 3 (destructive): writes to the `decisions` table stop
+        // here. New decisions live only in the `memories` table; the projection
+        // regen below sources from memories (Stage 2a). The decisions table
+        // remains for backwards-compat reads (queryDecisions, md-importer,
+        // commands-inspect, workflow-manifest) until #5756 drops it.
+        //
+        // Reversal: a code revert of this change restores the upsertDecision
+        // call. Memory rows written between merge and revert stay durable; the
+        // legacy table simply doesn't grow during the cutover window.
+        const id = nextDecisionIdAcrossSurfaces(adapter);
+        // The mirror-to-memories write is what persists the new decision. Must
+        // run before the projection regen — the regen sources from memories
+        // (Stage 2a) and would otherwise miss the just-saved decision. Pass
+        // the normalized field set so defaults (revisable, made_by, source)
+        // are recorded on the memory row.
+        await mirrorDecisionToMemory(id, normalized);
+        // Fetch all decisions (including superseded for the full register).
+        // ADR-013 Stage 2a: source from the `memories` table. The Phase 5
+        // dual-write keeps memories in sync with each decision save; the backfill
+        // (memory-backfill.ts) absorbs the historical chain and drift-heals
+        // superseded_by on every session start.
+        const { getAllDecisionsFromMemories } = await import('./context-store.js');
+        let allDecisions = getAllDecisionsFromMemories();
+        if (!allDecisions.some(d => d.id === id)) {
+            logWarning('projection', 'just-saved decision missing from memories after mirror; injecting fallback for projection', {
+                fn: 'saveDecisionToDb',
+                decisionId: id,
             });
-            return nextId;
-        });
-        // Fetch all decisions (including superseded for the full register)
-        let allDecisions = [];
-        if (adapter) {
-            const rows = adapter.prepare('SELECT * FROM decisions ORDER BY seq').all();
-            allDecisions = rows.map(row => ({
-                seq: row['seq'],
-                id: row['id'],
-                when_context: row['when_context'],
-                scope: row['scope'],
-                decision: row['decision'],
-                choice: row['choice'],
-                rationale: row['rationale'],
-                revisable: row['revisable'],
-                made_by: row['made_by'] ?? 'agent',
-                superseded_by: row['superseded_by'] ?? null,
-            }));
+            const nextSeq = allDecisions.reduce((max, d) => Math.max(max, d.seq ?? 0), 0) + 1;
+            const fallback = {
+                seq: nextSeq,
+                id,
+                when_context: normalized.when_context,
+                scope: normalized.scope,
+                decision: normalized.decision,
+                choice: normalized.choice,
+                rationale: normalized.rationale,
+                revisable: normalized.revisable,
+                made_by: normalized.made_by,
+                superseded_by: null,
+            };
+            allDecisions = [...allDecisions, fallback];
         }
         const filePath = resolveGsdRootFile(basePath, 'DECISIONS');
         // Check if existing DECISIONS.md has freeform (non-table) content.
@@ -460,51 +523,6 @@ export async function saveDecisionToDb(fields, basePath) {
         invalidateStateCache();
         clearPathCache();
         clearParseCache();
-        // ADR-013 dual-write: keep the memory store in sync with every decision
-        // persisted via the legacy gsd_save_decision path. Without this, prompts
-        // that still call gsd_save_decision (discuss.md, plan-milestone.md,
-        // plan-slice.md, et al.) would create decisions rows invisible to
-        // memory_query and loadMemoryBlock.
-        // Best-effort — never throw, never roll back the decision on failure.
-        try {
-            const { createMemory } = await import('./memory-store.js');
-            const decisionText = (fields.decision ?? '').trim();
-            const choiceText = (fields.choice ?? '').trim();
-            const rationaleText = (fields.rationale ?? '').trim();
-            const contentParts = [];
-            if (decisionText)
-                contentParts.push(decisionText);
-            if (choiceText)
-                contentParts.push(`Chose: ${choiceText}.`);
-            if (rationaleText)
-                contentParts.push(`Rationale: ${rationaleText}.`);
-            const content = contentParts.join(' ').slice(0, 600);
-            if (content) {
-                createMemory({
-                    category: 'architecture',
-                    content,
-                    scope: fields.scope || 'project',
-                    confidence: 0.85,
-                    structuredFields: {
-                        sourceDecisionId: id,
-                        when_context: fields.when_context ?? '',
-                        scope: fields.scope,
-                        decision: fields.decision,
-                        choice: fields.choice,
-                        rationale: fields.rationale,
-                        made_by: fields.made_by ?? 'agent',
-                        revisable: fields.revisable ?? '',
-                    },
-                });
-            }
-        }
-        catch (mirrorErr) {
-            logError('manifest', 'memory-store mirror write failed (non-fatal)', {
-                fn: 'saveDecisionToDb',
-                decisionId: id,
-                error: String(mirrorErr.message),
-            });
-        }
         return { id };
     }
     catch (err) {
@@ -515,6 +533,54 @@ export async function saveDecisionToDb(fields, basePath) {
         release();
     }
 }
+/**
+ * ADR-013 dual-write — mirror a freshly-saved decision into the `memories`
+ * table so the memory store remains the single source of truth for the
+ * DECISIONS.md projection (Stage 2a) and for prompt-inline reads (Stage 1).
+ *
+ * Best-effort mirror: logs failures without throwing to avoid blocking saves.
+ * Caller invokes this AFTER the decisions-table write completes and
+ * BEFORE the projection regen — the regen sources from memories and would
+ * otherwise miss the just-saved decision.
+ */
+async function mirrorDecisionToMemory(id, normalizedFields) {
+    try {
+        const { createMemory } = await import('./memory-store.js');
+        const { synthesizeDecisionMemoryContent } = await import('./memory-backfill.js');
+        const content = synthesizeDecisionMemoryContent(normalizedFields);
+        if (!content)
+            return false;
+        createMemory({
+            category: 'architecture',
+            content,
+            scope: normalizedFields.scope || 'project',
+            confidence: 0.85,
+            structuredFields: {
+                sourceDecisionId: id,
+                when_context: normalizedFields.when_context,
+                scope: normalizedFields.scope,
+                decision: normalizedFields.decision,
+                choice: normalizedFields.choice,
+                rationale: normalizedFields.rationale,
+                made_by: normalizedFields.made_by,
+                revisable: normalizedFields.revisable,
+                // New decisions are always written as active; md-importer can later
+                // set superseded_by on the source decision row, and the backfill's
+                // drift auto-heal pass propagates that update to this memory.
+                superseded_by: null,
+            },
+        });
+        return true;
+    }
+    catch (mirrorErr) {
+        logError('manifest', 'memory-store mirror write failed', {
+            fn: 'saveDecisionToDb',
+            decisionId: id,
+            error: String(mirrorErr.message),
+        });
+        return false;
+    }
+}
 /**
  * Extract a milestone/slice reference from a deferral decision.
  *

package/dist/resources/extensions/gsd/dispatch-guard.js

@@ -4,7 +4,7 @@ import { findMilestoneIds } from "./guided-flow.js";
 import { parseUnitId } from "./unit-id.js";
 import { isDbAvailable, getMilestoneSlices, getMilestone } from "./gsd-db.js";
 import { parseRoadmap } from "./parsers-legacy.js";
-import { isClosedStatus } from "./status-guards.js";
+import { isClosedStatus, isSkippedForDispatch } from "./status-guards.js";
 import { classifyMilestoneSummaryContent } from "./milestone-summary-classifier.js";
 import { readFileSync } from "node:fs";
 const SLICE_DISPATCH_TYPES = new Set([
@@ -49,7 +49,7 @@ export function getPriorSliceCompletionBlocker(base, _mainBranch, unitType, unit
         //      DB-backed projects must not treat SUMMARY.md as authoritative.
         if (isDbAvailable()) {
             const milestoneRow = getMilestone(mid);
-            if (milestoneRow && isClosedStatus(milestoneRow.status))
+            if (milestoneRow && isSkippedForDispatch(milestoneRow.status))
                 continue;
         }
         else {

package/dist/resources/extensions/gsd/docs/preferences-reference.md

@@ -100,7 +100,7 @@ Setting `prefer_skills: []` does **not** disable skill discovery — it just mea
 
 - `skill_rules`: situational rules with a human-readable `when` trigger and one or more of `use`, `prefer`, or `avoid`.
 
-- `custom_instructions`: extra durable instructions related to skill use. For operational project knowledge (recurring rules, gotchas, patterns), use `.gsd/KNOWLEDGE.md` instead — it's injected into every agent prompt automatically and agents can append to it during execution.
+- `custom_instructions`: extra durable instructions related to skill use. For operational project knowledge, use `.gsd/KNOWLEDGE.md` instead. Rules are file-canonical; patterns and lessons are persisted to the `memories` table and projected back into `KNOWLEDGE.md` on the next session start.
 
 - `language`: preferred response language for all GSD interactions. Accepts any language name or code — `"Chinese"`, `"zh"`, `"German"`, `"de"`, `"日本語"`, etc. When set, GSD injects "Always respond in \<language\>" into every agent's system prompt, including after `/clear`. Quickest way to set it: `/gsd language <name>`. To clear: `/gsd language off`.
 

package/dist/resources/extensions/gsd/doctor-git-checks.js

@@ -1,3 +1,5 @@
+// GSD-2 doctor git health checks
+import { spawnSync } from "node:child_process";
 import { existsSync, readdirSync, realpathSync, rmSync, statSync } from "node:fs";
 import { join, sep } from "node:path";
 import { loadFile } from "./files.js";
@@ -48,6 +50,23 @@ function isSameOrNestedPath(candidate, container) {
     return normalizedCandidate === normalizedContainer ||
         normalizedCandidate.startsWith(`${normalizedContainer}/`);
 }
+function getSnapshotDiffCheckFailure(basePath) {
+    const failures = [];
+    for (const args of [["--cached"], []]) {
+        const result = spawnSync("git", ["diff", "--check", ...args], {
+            cwd: basePath,
+            encoding: "utf-8",
+        });
+        if (result.status === 0)
+            continue;
+        const output = [result.stdout, result.stderr, result.error?.message]
+            .filter(Boolean)
+            .join("\n")
+            .trim();
+        failures.push(output || `git diff --check ${args.join(" ")} failed`);
+    }
+    return failures.length > 0 ? failures.join("\n") : null;
+}
 async function isCompletedMilestoneTerminal(basePath, milestoneId) {
     const summaryPath = resolveMilestoneFile(basePath, milestoneId, "SUMMARY");
     if (!summaryPath)
@@ -401,16 +420,32 @@ export async function checkGitHealth(basePath, issues, fixesApplied, shouldFix,
                         message: `Uncommitted changes detected with no commit in ${mins} minute${mins === 1 ? "" : "s"} (threshold: ${thresholdMinutes}m). Snapshotting tracked files.`,
                         fixable: true,
                     });
+                    const diffCheckFailure = getSnapshotDiffCheckFailure(basePath);
+                    if (diffCheckFailure) {
+                        issues.push({
+                            severity: "error",
+                            code: "conflict_markers_in_tracked_files",
+                            scope: "project",
+                            unitId: "project",
+                            message: `Cannot create gsd snapshot: tracked changes contain conflict markers or whitespace errors. Resolve conflicts manually before auto-mode can proceed.\n${diffCheckFailure}`,
+                            fixable: false,
+                        });
+                    }
                     if (shouldFix("stale_uncommitted_changes")) {
                         try {
-                            nativeAddTracked(basePath);
-                            const commitMsg = `gsd snapshot: uncommitted changes after ${mins}m inactivity`;
-                            const result = nativeCommit(basePath, commitMsg);
-                            if (result) {
-                                fixesApplied.push(`created gsd snapshot after ${mins}m of uncommitted changes`);
+                            if (diffCheckFailure) {
+                                fixesApplied.push("gsd snapshot skipped - conflict markers detected in tracked files");
                             }
                             else {
-                                fixesApplied.push("gsd snapshot skipped — nothing to commit after staging tracked files");
+                                nativeAddTracked(basePath);
+                                const commitMsg = `gsd snapshot: uncommitted changes after ${mins}m inactivity`;
+                                const result = nativeCommit(basePath, commitMsg);
+                                if (result) {
+                                    fixesApplied.push(`created gsd snapshot after ${mins}m of uncommitted changes`);
+                                }
+                                else {
+                                    fixesApplied.push("gsd snapshot skipped — nothing to commit after staging tracked files");
+                                }
                             }
                         }
                         catch {

package/dist/resources/extensions/gsd/doctor-runtime-checks.js

@@ -5,7 +5,7 @@ import { milestonesDir, gsdRoot, resolveGsdRootFile } from "./paths.js";
 import { deriveState, isGhostMilestone, isReusableGhostMilestone } from "./state.js";
 import { saveFile } from "./files.js";
 import { nativeIsRepo, nativeForEachRef, nativeUpdateRef } from "./native-git-bridge.js";
-import { readCrashLock, isLockProcessAlive, clearLock } from "./crash-recovery.js";
+import { readCrashLock, isLockProcessAlive, clearStaleWorkerLock } from "./crash-recovery.js";
 import { getActiveAutoWorkers } from "./db/auto-workers.js";
 import { normalizeRealPath } from "./paths.js";
 import { ensureGitignore, isGsdGitignored } from "./gitignore.js";
@@ -46,7 +46,7 @@ export async function checkRuntimeHealth(basePath, issues, fixesApplied, shouldF
                     fixable: true,
                 });
                 if (shouldFix("stale_crash_lock")) {
-                    clearLock(basePath);
+                    clearStaleWorkerLock(basePath);
                     fixesApplied.push("cleared stale auto-mode worker state");
                 }
             }
@@ -70,15 +70,32 @@ export async function checkRuntimeHealth(basePath, issues, fixesApplied, shouldF
                 // heartbeat for this project?" — readCrashLock returns null for
                 // healthy live workers (it surfaces stale ones only), so we must
                 // consult getActiveAutoWorkers directly.
-                const projectRoot = normalizeRealPath(basePath);
-                const activeWorkers = getActiveAutoWorkers().filter((w) => w.project_root_realpath === projectRoot && isLockProcessAlive({
-                    pid: w.pid,
-                    startedAt: w.started_at,
-                    unitType: "starting",
-                    unitId: "bootstrap",
-                    unitStartedAt: w.started_at,
-                }));
-                const lockHolderAlive = activeWorkers.length > 0;
+                let lockHolderAlive = false;
+                try {
+                    const projectRoot = normalizeRealPath(basePath);
+                    for (const worker of getActiveAutoWorkers()) {
+                        if (worker.project_root_realpath !== projectRoot)
+                            continue;
+                        try {
+                            if (isLockProcessAlive({
+                                pid: worker.pid,
+                                startedAt: worker.started_at,
+                                unitType: "starting",
+                                unitId: "bootstrap",
+                                unitStartedAt: worker.started_at,
+                            })) {
+                                lockHolderAlive = true;
+                                break;
+                            }
+                        }
+                        catch {
+                            // Ignore malformed worker rows or transient PID probe failures.
+                        }
+                    }
+                }
+                catch {
+                    // If worker lookup fails, continue with the stranded lock diagnosis.
+                }
                 if (!lockHolderAlive) {
                     issues.push({
                         severity: "error",