gsd-pi 2.82.0 → 3.0.0-dev.8b8d129d7

package/src/resources/extensions/gsd/db/milestone-leases.ts

@@ -255,6 +255,32 @@ export function releaseMilestoneLease(
   });
 }
 
+/**
+ * Force-release all held leases for a worker.
+ *
+ * Used by crash recovery once PID liveness has confirmed the worker is dead.
+ * No fencing token is required because this path is cleanup-only for a
+ * non-running process.
+ */
+export function forceReleaseLeasesForWorker(workerId: string): number {
+  if (!isDbAvailable()) return 0;
+  const db = _getAdapter()!;
+  let changes = 0;
+  transaction(() => {
+    const result = db.prepare(
+      `UPDATE milestone_leases
+       SET status = 'released'
+       WHERE worker_id = :worker_id
+         AND status = 'held'`,
+    ).run({ ":worker_id": workerId });
+    changes =
+      typeof (result as { changes?: unknown }).changes === "number"
+        ? (result as { changes: number }).changes
+        : 0;
+  });
+  return changes;
+}
+
 /**
  * Read current lease row for diagnostics. Returns null if no row exists.
  */

package/src/resources/extensions/gsd/db/unit-dispatches.ts

@@ -524,17 +524,18 @@ export function getRecentUnitKeysForProjectRoot(
   if (!isDbAvailable()) return [];
   const db = _getAdapter()!;
   const rows = db.prepare(
-    `SELECT ud.unit_id
+    `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,
-  }) as Array<{ unit_id: string }>;
-  return rows.reverse().map((r) => ({ key: r.unit_id }));
+  }) as Array<{ unit_type: string; unit_id: string }>;
+  return rows.reverse().map((r) => ({ key: `${r.unit_type}/${r.unit_id}` }));
 }
 
 /**

package/src/resources/extensions/gsd/db-base-schema.ts

@@ -168,6 +168,7 @@ export function createBaseSchemaObjects(db: DbAdapter, hooks: BaseSchemaHooks):
       proof_level TEXT NOT NULL DEFAULT '',
       integration_closure TEXT NOT NULL DEFAULT '',
       observability_impact TEXT NOT NULL DEFAULT '',
+      target_repositories TEXT NOT NULL DEFAULT '[]',
       sequence INTEGER DEFAULT 0,
       replan_triggered_at TEXT DEFAULT NULL,
       is_sketch INTEGER NOT NULL DEFAULT 0,
@@ -208,6 +209,7 @@ export function createBaseSchemaObjects(db: DbAdapter, hooks: BaseSchemaHooks):
       expected_output TEXT NOT NULL DEFAULT '[]',
       observability_impact TEXT NOT NULL DEFAULT '',
       full_plan_md TEXT NOT NULL DEFAULT '',
+      target_repositories TEXT NOT NULL DEFAULT '[]',
       sequence INTEGER DEFAULT 0,
       PRIMARY KEY (milestone_id, slice_id, id),
       FOREIGN KEY (milestone_id, slice_id) REFERENCES slices(milestone_id, id)

package/src/resources/extensions/gsd/db-migration-steps.ts

@@ -424,6 +424,11 @@ export function applyMigrationV28MemoryLastHitAt(db: DbAdapter): void {
   ensureColumn(db, "memories", "last_hit_at", "ALTER TABLE memories ADD COLUMN last_hit_at TEXT DEFAULT NULL");
 }
 
+export function applyMigrationV29RepositoryTargets(db: DbAdapter): void {
+  ensureColumn(db, "slices", "target_repositories", "ALTER TABLE slices ADD COLUMN target_repositories TEXT NOT NULL DEFAULT '[]'");
+  ensureColumn(db, "tasks", "target_repositories", "ALTER TABLE tasks ADD COLUMN target_repositories TEXT NOT NULL DEFAULT '[]'");
+}
+
 export interface MigrationV22Hooks {
   copyQualityGateRowsToRepairedTable(db: DbAdapter): void;
 }

package/src/resources/extensions/gsd/db-task-slice-rows.ts

@@ -22,6 +22,7 @@ export interface SliceRow {
   replan_triggered_at: string | null;
   is_sketch: number;
   sketch_scope: string;
+  target_repositories?: string[];
 }
 
 export interface TaskRow {
@@ -55,6 +56,7 @@ export interface TaskRow {
   escalation_awaiting_review: number;
   escalation_artifact_path: string | null;
   escalation_override_applied_at: string | null;
+  target_repositories?: string[];
 }
 
 type DbRow = Record<string, unknown>;
@@ -107,6 +109,7 @@ export function rowToSlice(row: DbRow): SliceRow {
     replan_triggered_at: (row["replan_triggered_at"] as string) ?? null,
     is_sketch: (row["is_sketch"] as number) ?? 0,
     sketch_scope: (row["sketch_scope"] as string) ?? "",
+    target_repositories: parseTaskArrayColumn(row["target_repositories"]),
   };
 }
 
@@ -142,5 +145,6 @@ export function rowToTask(row: DbRow): TaskRow {
     escalation_awaiting_review: (row["escalation_awaiting_review"] as number) ?? 0,
     escalation_artifact_path: (row["escalation_artifact_path"] as string) ?? null,
     escalation_override_applied_at: (row["escalation_override_applied_at"] as string) ?? null,
+    target_repositories: parseTaskArrayColumn(row["target_repositories"]),
   };
 }

package/src/resources/extensions/gsd/db-writer.ts

@@ -235,14 +235,63 @@ export async function nextDecisionId(): Promise<string> {
   }
 }
 
-/** Synchronous variant for use inside db.transaction(). */
-function nextDecisionIdSync(adapter: ReturnType<typeof import('./gsd-db.js')._getAdapter>): string {
+/**
+ * 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: ReturnType<typeof import('./gsd-db.js')._getAdapter>,
+): string {
   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'] as number | null) : 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'] as number | null) : 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() as Array<{ structured_fields: string | null }>;
+    for (const row of rows) {
+      if (!row.structured_fields) continue;
+      let sf: Record<string, unknown>;
+      try {
+        sf = JSON.parse(row.structured_fields) as Record<string, unknown>;
+      } 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')}`;
 }
@@ -416,6 +465,16 @@ export interface SaveDecisionFields {
   source?: string;
 }
 
+type NormalizedSaveDecisionFields = Omit<
+  SaveDecisionFields,
+  'when_context' | 'revisable' | 'made_by' | 'source'
+> & {
+  when_context: string;
+  revisable: string;
+  made_by: NonNullable<SaveDecisionFields['made_by']>;
+  source: string;
+};
+
 /**
  * Save a new decision to DB and regenerate DECISIONS.md.
  * Auto-assigns the next ID via nextDecisionId().
@@ -445,44 +504,59 @@ export async function saveDecisionToDb(
 
   try {
     const db = await import('./gsd-db.js');
-
     const adapter = db._getAdapter();
+    const normalized: NormalizedSaveDecisionFields = {
+      ...fields,
+      when_context: fields.when_context ?? '',
+      revisable: fields.revisable ?? 'Yes',
+      made_by: fields.made_by ?? 'agent',
+      source: fields.source ?? 'discussion',
+    };
 
-    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,
+    // 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: Decision[] = 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: Decision[] = [];
-    if (adapter) {
-      const rows = adapter.prepare('SELECT * FROM decisions ORDER BY seq').all();
-      allDecisions = rows.map(row => ({
-        seq: row['seq'] as number,
-        id: row['id'] as string,
-        when_context: row['when_context'] as string,
-        scope: row['scope'] as string,
-        decision: row['decision'] as string,
-        choice: row['choice'] as string,
-        rationale: row['rationale'] as string,
-        revisable: row['revisable'] as string,
-        made_by: (row['made_by'] as string as import('./types.js').DecisionMadeBy) ?? 'agent',
-        superseded_by: (row['superseded_by'] as string) ?? null,
-      }));
+      const nextSeq = allDecisions.reduce((max, d) => Math.max(max, d.seq ?? 0), 0) + 1;
+      const fallback: Decision = {
+        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');
@@ -538,48 +612,6 @@ export async function saveDecisionToDb(
     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: string[] = [];
-      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 as Error).message),
-      });
-    }
-
     return { id };
   } catch (err) {
     logError('manifest', 'saveDecisionToDb failed', { fn: 'saveDecisionToDb', error: String((err as Error).message) });
@@ -589,6 +621,57 @@ export async function saveDecisionToDb(
   }
 }
 
+/**
+ * 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: string,
+  normalizedFields: NormalizedSaveDecisionFields,
+): Promise<boolean> {
+  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 as Error).message),
+    });
+    return false;
+  }
+}
+
 /**
  * Extract a milestone/slice reference from a deferral decision.
  *

package/src/resources/extensions/gsd/dispatch-guard.ts

@@ -5,9 +5,10 @@ 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";
+import type { LoopState } from "./auto/types.js";
 
 const SLICE_DISPATCH_TYPES = new Set([
   "research-slice",
@@ -17,6 +18,63 @@ const SLICE_DISPATCH_TYPES = new Set([
   "complete-slice",
 ]);
 
+const CONSECUTIVE_SAME_UNIT_CAP_TYPES = new Set([
+  "complete-milestone",
+  "validate-milestone",
+  "research-slice",
+]);
+const CONSECUTIVE_SAME_UNIT_CAP = 2;
+
+type ConsecutiveDispatchState = Pick<
+  LoopState,
+  "consecutiveDispatchCount" | "lastDispatchedKey" | "lastDispatchPhase"
+>;
+
+/**
+ * Prevent repeated dispatches of the same unit within the same phase.
+ *
+ * Applies only to unit types in `CONSECUTIVE_SAME_UNIT_CAP_TYPES`. The first
+ * dispatch for a unit/phase pair starts a counter, unit or phase changes reset
+ * tracking, and dispatch is blocked once the counter reaches
+ * `CONSECUTIVE_SAME_UNIT_CAP`.
+ *
+ * Side effects: mutates `state.consecutiveDispatchCount`,
+ * `state.lastDispatchedKey`, and `state.lastDispatchPhase`.
+ *
+ * Returns `null` when dispatch is allowed, or a blocker message (including
+ * guidance to run `/gsd resume`) when the cap is reached.
+ */
+export function getConsecutiveDispatchBlocker(
+  state: ConsecutiveDispatchState,
+  phase: string,
+  unitType: string,
+  unitId: string,
+): string | null {
+  if (!CONSECUTIVE_SAME_UNIT_CAP_TYPES.has(unitType)) return null;
+  if (!state.consecutiveDispatchCount) state.consecutiveDispatchCount = new Map<string, number>();
+
+  const key = `${unitType}:${unitId}`;
+  const phaseChanged = state.lastDispatchPhase !== phase;
+  const switchedUnit = state.lastDispatchedKey !== key;
+  if (phaseChanged || switchedUnit) {
+    state.consecutiveDispatchCount.clear();
+    state.consecutiveDispatchCount.set(key, 1);
+    state.lastDispatchedKey = key;
+    state.lastDispatchPhase = phase;
+    return null;
+  }
+
+  const count = state.consecutiveDispatchCount.get(key) ?? 0;
+  if (count >= CONSECUTIVE_SAME_UNIT_CAP) {
+    return `Cannot dispatch ${unitType} ${unitId}: dispatched ${count} consecutive times; same-unit repeat cap reached. Resolve via /gsd resume.`;
+  }
+
+  state.consecutiveDispatchCount.set(key, count + 1);
+  state.lastDispatchedKey = key;
+  state.lastDispatchPhase = phase;
+  return null;
+}
+
 export function getPriorSliceCompletionBlocker(
   base: string,
   _mainBranch: string,
@@ -58,7 +116,7 @@ export function getPriorSliceCompletionBlocker(
     //      DB-backed projects must not treat SUMMARY.md as authoritative.
     if (isDbAvailable()) {
       const milestoneRow = getMilestone(mid);
-      if (milestoneRow && isClosedStatus(milestoneRow.status)) continue;
+      if (milestoneRow && isSkippedForDispatch(milestoneRow.status)) continue;
     } else {
       const summaryPath = resolveMilestoneFile(base, mid, "SUMMARY");
       let summaryContent: string | null = null;

package/src/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`.
 
@@ -147,6 +147,14 @@ Setting `prefer_skills: []` does **not** disable skill discovery — it just mea
 
 - `unique_milestone_ids`: boolean — when `true`, generates milestone IDs in `M{seq}-{rand6}` format (e.g. `M001-eh88as`) instead of plain sequential `M001`. Prevents ID collisions in team workflows where multiple contributors create milestones concurrently. Both formats coexist — existing `M001`-style milestones remain valid. Default: `false`.
 
+- `workspace`: optional parent-workspace repository registry. Keys:
+  - `mode`: `"project"` or `"parent"` — registry mode for repository lookup. Default: `"project"`.
+  - `repositories`: object keyed by repository id. A default `"project"` repository pointing at the project root is always available, even when not listed here (and can be overridden by explicitly defining `"project"`). Each repository supports:
+    - `path`: string — repository root path relative to project root.
+    - `role`: string — optional human label for prompts/reporting.
+    - `verification`: string[] — optional default verification commands.
+    - `commit_policy`: `"auto"` or `"skip"` — optional turn-commit policy for auto-mode commit actions. Defaults to `"auto"` when omitted. `"skip"` suppresses commit execution for that target repo.
+
 - `budget_ceiling`: number — maximum dollar amount to spend on auto-mode. When reached, behavior is controlled by `budget_enforcement`. Default: no limit.
 
 - `budget_enforcement`: `"warn"`, `"pause"`, or `"halt"` — action taken when `budget_ceiling` is reached.

package/src/resources/extensions/gsd/doctor-git-checks.ts

@@ -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";
 
@@ -7,7 +9,7 @@ import { parseRoadmap as parseLegacyRoadmap } from "./parsers-legacy.js";
 import { isDbAvailable, getMilestone } from "./gsd-db.js";
 import { resolveMilestoneFile } from "./paths.js";
 import { deriveState, isMilestoneComplete } from "./state.js";
-import { listWorktrees, resolveGitDir, worktreesDir } from "./worktree-manager.js";
+import { createWorktree, listWorktrees, resolveGitDir, worktreesDir } from "./worktree-manager.js";
 import { abortAndReset } from "./git-self-heal.js";
 import { RUNTIME_EXCLUSION_PATHS, resolveMilestoneIntegrationBranch, writeIntegrationBranch } from "./git-service.js";
 import { nativeIsRepo, nativeWorktreeList, nativeWorktreeRemove, nativeBranchList, nativeBranchDelete, nativeLsFiles, nativeRmCached, nativeHasChanges, nativeLastCommitEpoch, nativeGetCurrentBranch, nativeAddTracked, nativeCommit } from "./native-git-bridge.js";
@@ -52,6 +54,39 @@ function isSameOrNestedPath(candidate: string, container: string): boolean {
     normalizedCandidate.startsWith(`${normalizedContainer}/`);
 }
 
+function hasProjectContentOnDisk(dirPath: string): boolean {
+  try {
+    for (const entry of readdirSync(dirPath, { withFileTypes: true })) {
+      if (entry.name === ".git" || entry.name === ".gsd") continue;
+      if (entry.name === ".DS_Store") continue;
+      return true;
+    }
+  } catch {
+    return false;
+  }
+  return false;
+}
+
+function getSnapshotDiffCheckFailure(basePath: string): string | null {
+  const failures: string[] = [];
+
+  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: string, milestoneId: string): Promise<boolean> {
   const summaryPath = resolveMilestoneFile(basePath, milestoneId, "SUMMARY");
   if (!summaryPath) return false;
@@ -101,6 +136,37 @@ export async function checkGitHealth(
         ? await isCompletedMilestoneTerminal(basePath, milestoneId)
         : false;
 
+      if (!isComplete && !hasProjectContentOnDisk(wt.path) && hasProjectContentOnDisk(basePath)) {
+        issues.push({
+          severity: "error",
+          code: "worktree_empty_with_project_content",
+          scope: "milestone",
+          unitId: milestoneId,
+          message: `Worktree ${wt.path} has no project content, but project root ${basePath} does. Run doctor --fix to recreate the worktree.`,
+          fixable: true,
+        });
+
+        if (shouldFix("worktree_empty_with_project_content")) {
+          try {
+            nativeWorktreeRemove(basePath, wt.path, true);
+            const recreated = createWorktree(basePath, milestoneId, {
+              branch: wt.branch,
+              reuseExistingBranch: true,
+            });
+            const reset = spawnSync("git", ["reset", "--hard"], {
+              cwd: recreated.path,
+              encoding: "utf-8",
+            });
+            if (reset.status !== 0) {
+              throw new Error(reset.stderr || reset.error?.message || "git reset --hard failed");
+            }
+            fixesApplied.push(`recreated empty worktree ${wt.path}`);
+          } catch {
+            fixesApplied.push(`failed to recreate empty worktree ${wt.path}`);
+          }
+        }
+      }
+
       if (isComplete) {
         issues.push({
           severity: "warning",
@@ -411,15 +477,31 @@ export async function checkGitHealth(
             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 {
               fixesApplied.push("failed to create gsd snapshot commit");