gsd-pi 2.80.0-dev.c5f2443b3 → 2.80.0-dev.e146beb20

package/src/resources/extensions/gsd/bootstrap/write-gate.ts

@@ -1,10 +1,12 @@
-import { copyFileSync, existsSync, mkdirSync, readFileSync, renameSync, unlinkSync, writeFileSync } from "node:fs";
+import { copyFileSync, existsSync, mkdirSync, readFileSync, realpathSync, renameSync, unlinkSync, writeFileSync } from "node:fs";
 import { isAbsolute, join, relative, resolve, sep } from "node:path";
 
 import { minimatch } from "minimatch";
 
+import { getIsolationMode } from "../preferences.js";
 import type { ToolsPolicy } from "../unit-context-manifest.js";
 import { logWarning } from "../workflow-logger.js";
+import { isGsdWorktreePath, resolveWorktreeProjectRoot } from "../worktree-root.js";
 
 /**
  * Regex matching milestone CONTEXT.md file names in both legacy M001
@@ -882,3 +884,135 @@ export function shouldBlockPlanningUnit(
   // avoids breaking gsd_* MCP tools or future safe additions.
   return { block: false };
 }
+
+// ─── Worktree isolation write gate (#5199) ────────────────────────────────
+//
+// When `git.isolation: worktree` is configured, the per-unit commit pipeline
+// only runs inside the auto-mode loop (`auto-post-unit.ts`). If the LLM
+// authors code at the project root before auto-mode is started, those writes
+// land in the working tree but never reach a commit — they're silently
+// orphaned outside git history. This guard blocks those writes at the
+// tool_call seam so the agent receives a clear error instead.
+
+const WORKTREE_GATE_BOOTSTRAP_UNITS = new Set([
+  "discuss-milestone",
+  "plan-milestone",
+  "init",
+]);
+
+function realpathOrResolve(p: string): string {
+  const abs = resolve(p);
+  try {
+    return realpathSync(abs);
+  } catch {
+    // Path doesn't exist (yet) — realpath the deepest existing ancestor so
+    // platforms where /tmp -> /private/tmp don't break containment checks.
+    let dir = abs;
+    const tail: string[] = [];
+    while (dir && dir !== resolve(dir, "..")) {
+      try {
+        const real = realpathSync(dir);
+        return tail.length ? join(real, ...tail.reverse()) : real;
+      } catch {
+        const idx = dir.lastIndexOf(sep);
+        if (idx <= 0) break;
+        tail.push(dir.slice(idx + 1));
+        dir = dir.slice(0, idx) || sep;
+      }
+    }
+    return abs;
+  }
+}
+
+function isPathContained(target: string, container: string): boolean {
+  if (target === container) return true;
+  return target.startsWith(container.endsWith(sep) ? container : container + sep);
+}
+
+/**
+ * Block planning-write tool calls that would land code at the project root
+ * while `git.isolation: worktree` is in effect and auto-mode hasn't created
+ * (or flipped cwd into) the milestone worktree.
+ *
+ * Pure / unit-testable. Callers in `register-hooks.ts` supply the resolved
+ * project root and current auto liveness; this function does no I/O beyond
+ * realpath resolution.
+ *
+ * Allow rules (in order):
+ *   1. Tool isn't a planning-write (write/edit/multi_edit/notebook_edit).
+ *   2. `GSD_DISABLE_WORKTREE_WRITE_GUARD=1` self-hosting bypass.
+ *   3. Isolation mode is not "worktree".
+ *   4. Active unit is a bootstrap unit (discuss-milestone/plan-milestone/init).
+ *   5. Target is inside `<projectRoot>/.gsd/worktrees/` (a real worktree).
+ *   6. Target is inside `<projectRoot>/.gsd/` and isn't masquerading as a
+ *      worktrees sibling (rejects the `.gsd/worktrees-extra/…` prefix trick).
+ *   7. Auto is live AND `effectiveBasePath` is itself a `.gsd/worktrees/…` path.
+ *
+ * Otherwise: block with a message that points the agent at `/gsd` to start
+ * auto-mode.
+ */
+export function shouldBlockWorktreeWrite(
+  toolName: string,
+  targetPath: string,
+  effectiveBasePath: string,
+  isAutoLive: boolean,
+  currentUnitType?: string | null,
+): { block: boolean; reason?: string } {
+  const tool = canonicalToolName(toolName);
+  if (!PLANNING_WRITE_TOOLS.has(tool)) return { block: false };
+  if (process.env.GSD_DISABLE_WORKTREE_WRITE_GUARD === "1") return { block: false };
+  if (getIsolationMode(effectiveBasePath) !== "worktree") return { block: false };
+  if (currentUnitType && WORKTREE_GATE_BOOTSTRAP_UNITS.has(currentUnitType)) return { block: false };
+
+  if (!targetPath) {
+    return {
+      block: true,
+      reason: [
+        `HARD BLOCK: ${tool} called with empty path while \`git.isolation: worktree\` is configured`,
+        `and auto-mode is not active. Refusing to allow writes that cannot be located.`,
+      ].join(" "),
+    };
+  }
+
+  // Resolve the target relative to the project root, then realpath to defeat
+  // symlink-based escapes and prefix tricks (e.g. .gsd/worktrees-extra/).
+  const projectRoot = resolveWorktreeProjectRoot(effectiveBasePath);
+  const absTarget = isAbsolute(targetPath) ? targetPath : resolve(projectRoot, targetPath);
+  const realTarget = realpathOrResolve(absTarget);
+  const realRoot = realpathOrResolve(projectRoot);
+  const realGsd = realpathOrResolve(join(projectRoot, ".gsd"));
+  const realWorktreesDir = realpathOrResolve(join(projectRoot, ".gsd", "worktrees"));
+
+  // Allow writes inside the legitimate worktrees subtree.
+  if (isPathContained(realTarget, realWorktreesDir)) return { block: false };
+
+  // Allow writes to .gsd/ planning artifacts, but reject siblings whose name
+  // starts with "worktrees" (the worktrees-extra prefix trick — case 4).
+  if (isPathContained(realTarget, realGsd)) {
+    const rel = relative(realGsd, realTarget);
+    const firstSeg = rel.split(/[\/\\]/)[0] ?? "";
+    if (!firstSeg.startsWith("worktrees")) return { block: false };
+    // fall through: looks like worktrees<something> sibling — block
+  }
+
+  // Auto is live and the caller is operating inside a worktree path —
+  // host tool's write happens in worktree context; let it through.
+  if (isAutoLive && isGsdWorktreePath(effectiveBasePath)) return { block: false };
+
+  // Block. Provide enough context that the agent can self-correct.
+  const displayTarget = isPathContained(realTarget, realRoot)
+    ? relative(realRoot, realTarget) || "."
+    : realTarget;
+  return {
+    block: true,
+    reason: [
+      `HARD BLOCK: Worktree isolation is configured (\`git.isolation: worktree\`) but auto-mode is`,
+      `not running and the target "${displayTarget}" is not inside \`.gsd/worktrees/<MID>/\`.`,
+      `Code edits at the project root would be lost — only the auto-mode commit pipeline`,
+      `(auto-post-unit) commits work, and it never runs outside the loop.`,
+      `Required action: start auto-mode with \`/gsd\` so the milestone worktree is created,`,
+      `then write inside it. To disable this guard for self-hosting development, set`,
+      `GSD_DISABLE_WORKTREE_WRITE_GUARD=1.`,
+    ].join(" "),
+  };
+}

package/src/resources/extensions/gsd/clean-root-preflight.ts

@@ -21,10 +21,34 @@ import { nativeHasChanges } from "./native-git-bridge.js";
 export interface PreflightResult {
   /** true when a stash was pushed and postflightPopStash should be called */
   stashPushed: boolean;
+  /** Unique marker embedded in the stash message for targeted restoration */
+  stashMarker?: string;
   /** human-readable summary of what happened (empty string for clean trees) */
   summary: string;
 }
 
+function findPreflightStashRef(basePath: string, milestoneId: string, stashMarker?: string): string | null {
+  const markerPrefix = `gsd-preflight-stash:${milestoneId}:`;
+  let fallbackRef: string | null = null;
+  try {
+    const list = execFileSync("git", ["stash", "list", "--format=%gd%x00%s"], {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8",
+      env: GIT_NO_PROMPT_ENV,
+    });
+    for (const line of list.split("\n")) {
+      const [ref, subject] = line.split("\x00");
+      if (!ref || !subject) continue;
+      if (stashMarker && subject.includes(stashMarker)) return ref;
+      if (!fallbackRef && subject.includes(markerPrefix)) fallbackRef = ref;
+    }
+  } catch (err) {
+    logWarning("preflight", `stash list failed before restore: ${err instanceof Error ? err.message : String(err)}`);
+  }
+  return fallbackRef;
+}
+
 /**
  * Check the working tree for dirty files before a milestone merge.
  *
@@ -62,7 +86,8 @@ export function preflightCleanRoot(
 
   // Push the stash
   try {
-    execFileSync("git", ["stash", "push", "--include-untracked", "-m", "gsd-preflight-stash"], {
+    const stashMarker = `gsd-preflight-stash:${milestoneId}:${process.pid}:${Date.now()}:${process.hrtime.bigint().toString(36)}`;
+    execFileSync("git", ["stash", "push", "--include-untracked", "-m", `gsd-preflight-stash [${stashMarker}]`], {
       cwd: basePath,
       stdio: ["ignore", "pipe", "pipe"],
       encoding: "utf-8",
@@ -70,6 +95,7 @@ export function preflightCleanRoot(
     });
     return {
       stashPushed: true,
+      stashMarker,
       summary: `Stashed uncommitted changes before merge (milestone ${milestoneId}).`,
     };
   } catch (err) {
@@ -91,10 +117,19 @@ export function preflightCleanRoot(
 export function postflightPopStash(
   basePath: string,
   milestoneId: string,
+  stashMarker: string | undefined,
   notify: (message: string, level: "info" | "warning" | "error") => void,
 ): void {
+  let stashRef: string | null = null;
   try {
-    execFileSync("git", ["stash", "pop"], {
+    stashRef = findPreflightStashRef(basePath, milestoneId, stashMarker);
+    if (!stashRef) {
+      const msg = `No matching GSD preflight stash found for milestone ${milestoneId}; leaving stash list untouched.`;
+      logWarning("preflight", msg);
+      notify(msg, "warning");
+      return;
+    }
+    execFileSync("git", ["stash", "pop", stashRef], {
       cwd: basePath,
       stdio: ["ignore", "pipe", "pipe"],
       encoding: "utf-8",
@@ -104,7 +139,10 @@ export function postflightPopStash(
   } catch (err) {
     // Pop conflicts mean the merged code collides with the stashed changes.
     // Log a warning — the user needs to resolve manually, but the merge succeeded.
-    const msg = `git stash pop failed after merge of milestone ${milestoneId}: ${err instanceof Error ? err.message : String(err)}. Run "git stash pop" manually to restore your changes.`;
+    const restoreHint = stashRef
+      ? `Run "git stash pop ${stashRef}" or "git stash apply ${stashRef}" manually to restore the correct stash.`
+      : `Run "git stash list" to find the matching GSD preflight stash before restoring manually.`;
+    const msg = `git stash pop ${stashRef ?? ""}`.trim() + ` failed after merge of milestone ${milestoneId}: ${err instanceof Error ? err.message : String(err)}. ${restoreHint}`;
     logWarning("preflight", msg);
     notify(msg, "warning");
   }

package/src/resources/extensions/gsd/commands/dispatcher.ts

@@ -45,5 +45,11 @@ export async function handleGSDCommand(
 
   if (handled) return;
 
+  if (trimmed.includes(" ")) {
+    const { handleDo } = await import("../commands-do.js");
+    await handleDo(trimmed, ctx, pi);
+    return;
+  }
+
   ctx.ui.notify(`Unknown: /gsd ${trimmed}. Run /gsd help for available commands.`, "warning");
 }

package/src/resources/extensions/gsd/commands-extract-learnings.ts

@@ -222,14 +222,19 @@ Using the \`write\` tool, persist the full structured report to
 LEARNINGS.md is the full, cited audit trail. Write it first — subsequent steps
 feed from its content.
 
-### Step 3 — Optionally pre-query the memory store for semantic duplicates
+### Step 3 — Run one bounded duplicate check
 
-Before persisting any extracted item in Steps 4–6, you may call
-\`memory_query\` with 2–3 keywords from the item to check whether the
-memory store already holds a semantically equivalent entry at high
-confidence. Skip those items in their respective steps. The memory store
-is the single source of truth for cross-session durable knowledge — no
-other persistence call is part of this flow.
+Before persisting extracted items in Steps 4–6, do at most one duplicate-check
+pass for the durable Decisions, Lessons, and Patterns from this milestone. Use
+the already-written LEARNINGS.md content and call \`memory_query\` once with a
+compact keyword summary for the whole batch. If that result clearly shows a
+semantically equivalent high-confidence memory for an item, mark only that item
+as already captured and skip it in its respective persistence step.
+
+Do not re-read milestone artefacts or repeat memory queries category-by-category
+after this point. The memory store is the single source of truth for
+cross-session durable knowledge — no other persistence call is part of this
+flow.
 
 ### Step 4 — Persist Patterns via \`capture_thought\`
 
@@ -268,11 +273,11 @@ later projection back to a human-visible decisions register stays lossless
 
 ### Step 7 — Deduplication rule (applies to Steps 4, 5, 6)
 
-Before each \`capture_thought\` call, optionally call \`memory_query\` with 2–3
-keywords from the entry. If a semantically equivalent memory is returned at
-high confidence, skip the capture entirely. Prefer skipping a near-duplicate
-over creating a second slightly-different row — redundancy degrades the
-signal.
+Use only the duplicate-check result from Step 3. If that bounded check returned
+a semantically equivalent memory at high confidence for an extracted item, skip
+the capture entirely. Otherwise, persist the item once via \`capture_thought\`.
+Prefer skipping a near-duplicate over creating a second slightly-different row
+— redundancy degrades the signal.
 
 ### Step 8 — Surprises stay only in LEARNINGS.md
 

package/src/resources/extensions/gsd/crash-recovery.ts

@@ -38,6 +38,7 @@ import { _getAdapter, isDbAvailable } from "./gsd-db.js";
 import { gsdRoot, normalizeRealPath } from "./paths.js";
 import { atomicWriteSync } from "./atomic-write.js";
 import { effectiveLockFile } from "./session-lock.js";
+import { isInFlightRuntimePhase, listUnitRuntimeRecords, type AutoUnitRuntimeRecord } from "./unit-runtime.js";
 
 export interface LockData {
   pid: number;
@@ -103,10 +104,40 @@ function getLatestDispatchForWorker(workerId: string):
   return row ?? null;
 }
 
-function workerToLockData(worker: AutoWorkerRow): LockData {
+function latestInFlightRuntimeRecord(basePath: string): AutoUnitRuntimeRecord | null {
+  const records = listUnitRuntimeRecords(basePath).filter((record) =>
+    isInFlightRuntimePhase(record.phase),
+  );
+  if (records.length === 0) return null;
+  return records.sort((a, b) => {
+    const bTime = b.updatedAt || b.startedAt || 0;
+    const aTime = a.updatedAt || a.startedAt || 0;
+    return bTime - aTime;
+  })[0] ?? null;
+}
+
+function runtimeRecordToLockData(worker: AutoWorkerRow, record: AutoUnitRuntimeRecord, sessionFile?: string): LockData {
+  const startedAt = Number.isFinite(record.startedAt)
+    ? new Date(record.startedAt).toISOString()
+    : worker.started_at;
+  return {
+    pid: worker.pid,
+    startedAt: worker.started_at,
+    unitType: record.unitType,
+    unitId: record.unitId,
+    unitStartedAt: startedAt,
+    sessionFile,
+  };
+}
+
+function workerToLockData(basePath: string, worker: AutoWorkerRow): LockData {
   const dispatch = getLatestDispatchForWorker(worker.worker_id);
   const sessionFile =
     getRuntimeKv<string>("worker", worker.worker_id, SESSION_FILE_KV_KEY) ?? undefined;
+  if (!dispatch) {
+    const runtimeRecord = latestInFlightRuntimeRecord(basePath);
+    if (runtimeRecord) return runtimeRecordToLockData(worker, runtimeRecord, sessionFile);
+  }
   return {
     pid: worker.pid,
     startedAt: worker.started_at,
@@ -204,7 +235,7 @@ export function readCrashLock(basePath: string): LockData | null {
     try {
       const projectRoot = normalizeRealPath(basePath);
       const stale = findStaleWorkerForProject(projectRoot);
-      if (stale) return workerToLockData(stale);
+      if (stale) return workerToLockData(basePath, stale);
     } catch {
       // Fall through to the legacy lock-file compatibility path.
     }
@@ -260,25 +291,48 @@ export function formatCrashInfo(lock: LockData): string {
  */
 export function emitCrashRecoveredUnitEnd(basePath: string, lock: LockData): void {
   if (!lock.unitType || !lock.unitId || lock.unitType === "starting") return;
+  emitOpenUnitEndForUnit(basePath, lock.unitType, lock.unitId, "crash-recovered");
+}
 
+export function emitOpenUnitEndForUnit(
+  basePath: string,
+  unitType: string,
+  unitId: string,
+  status: string,
+  errorContext?: { message: string; category: string; stopReason?: string; isTransient?: boolean; retryAfterMs?: number },
+): boolean {
   try {
     const all = queryJournal(basePath);
 
     const starts = all.filter(
-      (e) => e.eventType === "unit-start" && e.data?.unitId === lock.unitId,
+      (e) =>
+        e.eventType === "unit-start" &&
+        e.data?.unitType === unitType &&
+        e.data?.unitId === unitId,
     );
-    if (starts.length === 0) return;
+    if (starts.length === 0) return false;
 
-    const lastStart = starts[starts.length - 1];
+    const lastStart = [...starts].reverse().find((start) => {
+      return !all.some(
+        (e) =>
+          e.eventType === "unit-end" &&
+          e.data?.unitType === unitType &&
+          e.data?.unitId === unitId &&
+          e.causedBy?.flowId === start.flowId &&
+          e.causedBy?.seq === start.seq,
+      );
+    });
+    if (!lastStart) return false;
 
     const alreadyClosed = all.some(
       (e) =>
         e.eventType === "unit-end" &&
-        e.data?.unitId === lock.unitId &&
+        e.data?.unitType === unitType &&
+        e.data?.unitId === unitId &&
         e.causedBy?.flowId === lastStart.flowId &&
         e.causedBy?.seq === lastStart.seq,
     );
-    if (alreadyClosed) return;
+    if (alreadyClosed) return false;
 
     const maxSeq = all
       .filter((e) => e.flowId === lastStart.flowId)
@@ -290,15 +344,18 @@ export function emitCrashRecoveredUnitEnd(basePath: string, lock: LockData): voi
       seq: maxSeq + 1,
       eventType: "unit-end",
       data: {
-        unitType: lock.unitType,
-        unitId: lock.unitId,
-        status: "crash-recovered",
+        unitType,
+        unitId,
+        status,
         artifactVerified: false,
+        ...(errorContext ? { errorContext } : {}),
       },
       causedBy: { flowId: lastStart.flowId, seq: lastStart.seq },
     });
+    return true;
   } catch {
     // Never throw from crash recovery path.
+    return false;
   }
 }
 

package/src/resources/extensions/gsd/custom-workflow-engine.ts

@@ -29,6 +29,7 @@ import {
   markStepActive,
   markStepComplete,
   expandIteration,
+  isTerminalStepStatus,
   type WorkflowGraph,
 } from "./graph.js";
 import { injectContext } from "./context-injector.js";
@@ -40,6 +41,24 @@ import { withFileLock } from "./file-lock.js";
 // Re-export for downstream consumers
 export { readFrozenDefinition } from "./definition-io.js";
 
+function formatBlockedWorkflowReason(graph: WorkflowGraph): string {
+  const statusById = new Map(graph.steps.map((step) => [step.id, step.status]));
+  const blockedSteps = graph.steps
+    .filter((step) => step.status === "pending")
+    .map((step) => {
+      const blockers = step.dependsOn
+        .filter((depId) => !isTerminalStepStatus(statusById.get(depId)))
+        .map((depId) => `${depId} (${statusById.get(depId) ?? "missing"})`);
+      return blockers.length > 0
+        ? `${step.id} waiting on ${blockers.join(", ")}`
+        : `${step.id} has no runnable dependency path`;
+    });
+
+  return blockedSteps.length > 0
+    ? `Workflow blocked: no pending steps are ready. Blocked steps: ${blockedSteps.join("; ")}`
+    : "Workflow blocked: no pending steps are ready.";
+}
+
 export class CustomWorkflowEngine implements WorkflowEngine {
   readonly engineId = "custom";
   private readonly runDir: string;
@@ -114,7 +133,11 @@ export class CustomWorkflowEngine implements WorkflowEngine {
           (step) => step.status === "complete" || step.status === "expanded",
         );
         if (!allDone) {
-          return { action: "skip" };
+          return {
+            action: "stop",
+            reason: formatBlockedWorkflowReason(graph),
+            level: "error",
+          };
         }
         return {
           action: "stop",

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

@@ -323,6 +323,20 @@ export function createBaseSchemaObjects(db: DbAdapter, hooks: BaseSchemaHooks):
     )
   `);
 
+  db.exec(`
+    CREATE TABLE IF NOT EXISTS milestone_commit_attributions (
+      commit_sha TEXT NOT NULL,
+      milestone_id TEXT NOT NULL,
+      slice_id TEXT DEFAULT NULL,
+      task_id TEXT DEFAULT NULL,
+      source TEXT NOT NULL DEFAULT 'recorded',
+      confidence REAL NOT NULL DEFAULT 1.0,
+      files_json TEXT NOT NULL DEFAULT '[]',
+      created_at TEXT NOT NULL DEFAULT '',
+      PRIMARY KEY (commit_sha, milestone_id)
+    )
+  `);
+
   db.exec(`
     CREATE TABLE IF NOT EXISTS audit_events (
       event_id TEXT PRIMARY KEY,
@@ -359,6 +373,7 @@ export function createBaseSchemaObjects(db: DbAdapter, hooks: BaseSchemaHooks):
   db.exec("CREATE INDEX IF NOT EXISTS idx_gate_runs_turn ON gate_runs(trace_id, turn_id)");
   db.exec("CREATE INDEX IF NOT EXISTS idx_gate_runs_lookup ON gate_runs(milestone_id, slice_id, task_id, gate_id)");
   db.exec("CREATE INDEX IF NOT EXISTS idx_turn_git_tx_turn ON turn_git_transactions(trace_id, turn_id)");
+  db.exec("CREATE INDEX IF NOT EXISTS idx_milestone_commit_attr_milestone ON milestone_commit_attributions(milestone_id)");
   db.exec("CREATE INDEX IF NOT EXISTS idx_audit_events_trace ON audit_events(trace_id, ts)");
   db.exec("CREATE INDEX IF NOT EXISTS idx_audit_events_turn ON audit_events(trace_id, turn_id, ts)");
 

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

@@ -399,6 +399,23 @@ export function applyMigrationV23MilestoneQueue(db: DbAdapter): void {
   ensureColumn(db, "milestones", "sequence", "ALTER TABLE milestones ADD COLUMN sequence INTEGER DEFAULT 0");
 }
 
+export function applyMigrationV26MilestoneCommitAttributions(db: DbAdapter): void {
+  db.exec(`
+    CREATE TABLE IF NOT EXISTS milestone_commit_attributions (
+      commit_sha TEXT NOT NULL,
+      milestone_id TEXT NOT NULL,
+      slice_id TEXT DEFAULT NULL,
+      task_id TEXT DEFAULT NULL,
+      source TEXT NOT NULL DEFAULT 'recorded',
+      confidence REAL NOT NULL DEFAULT 1.0,
+      files_json TEXT NOT NULL DEFAULT '[]',
+      created_at TEXT NOT NULL DEFAULT '',
+      PRIMARY KEY (commit_sha, milestone_id)
+    )
+  `);
+  db.exec("CREATE INDEX IF NOT EXISTS idx_milestone_commit_attr_milestone ON milestone_commit_attributions(milestone_id)");
+}
+
 export interface MigrationV22Hooks {
   copyQualityGateRowsToRepairedTable(db: DbAdapter): void;
 }