gsd-pi 2.76.0-dev.fe143342a → 2.77.0-dev.538325aea

package/src/resources/extensions/gsd/tests/workflow-tool-executors.test.ts

@@ -1,6 +1,6 @@
 import test from "node:test";
 import assert from "node:assert/strict";
-import { mkdirSync, rmSync, readFileSync, existsSync, writeFileSync } from "node:fs";
+import { mkdirSync, rmSync, readFileSync, existsSync, writeFileSync, unlinkSync } from "node:fs";
 import { join } from "node:path";
 import { tmpdir } from "node:os";
 import { randomUUID } from "node:crypto";
@@ -11,7 +11,7 @@ import {
   _getAdapter,
   insertGateRow,
 } from "../gsd-db.ts";
-import { markDepthVerified, clearDiscussionFlowState } from "../bootstrap/write-gate.ts";
+import { markDepthVerified, clearDiscussionFlowState, loadWriteGateSnapshot } from "../bootstrap/write-gate.ts";
 import {
   executeCompleteMilestone,
   executePlanMilestone,
@@ -742,3 +742,66 @@ test("executeSummarySave leaves sibling CONTEXT-DRAFT intact for non-CONTEXT art
     cleanup(base);
   }
 });
+
+test("executeSummarySave CONTEXT HARD BLOCK clears after write-gate state file is deleted (#4343)", async () => {
+  const base = makeTmpBase();
+  const originalEnv = process.env.GSD_PERSIST_WRITE_GATE_STATE;
+  process.env.GSD_PERSIST_WRITE_GATE_STATE = "1";
+  try {
+    openTestDb(base);
+    clearDiscussionFlowState();
+
+    // First call: CONTEXT artifact without depth verification → HARD BLOCK
+    const blocked = await inProjectDir(base, () => executeSummarySave({
+      milestone_id: "M001",
+      artifact_type: "CONTEXT",
+      content: "# Context\n\ncontent",
+    }, base));
+    assert.equal(blocked.isError, true, "should be blocked without depth verification");
+    assert.match(
+      blocked.content[0].text,
+      /HARD BLOCK/,
+      "blocked result should mention HARD BLOCK",
+    );
+
+    // Verify the state file was written (persist mode is active)
+    const stateFilePath = join(base, ".gsd", "runtime", "write-gate-state.json");
+    // The state file may or may not exist at this point (block doesn't write state).
+    // Write a fake state file simulating stale persisted block state.
+    mkdirSync(join(base, ".gsd", "runtime"), { recursive: true });
+    writeFileSync(stateFilePath, JSON.stringify({
+      verifiedDepthMilestones: [],
+      activeQueuePhase: false,
+      pendingGateId: "depth_verification_M001",
+    }));
+
+    // User deletes the state file to reset the block
+    unlinkSync(stateFilePath);
+    assert.ok(!existsSync(stateFilePath), "state file deleted");
+
+    // The snapshot loaded after deletion should be clean (no pending gate, no block)
+    const snapshot = loadWriteGateSnapshot(base);
+    assert.equal(snapshot.pendingGateId, null, "pendingGateId should be null after file deletion");
+    assert.deepEqual(snapshot.verifiedDepthMilestones, [], "verifiedDepthMilestones should be empty after file deletion");
+
+    // Depth-verify and re-attempt: should succeed after deletion clears stale state
+    markDepthVerified("M001", base);
+
+    const unblocked = await inProjectDir(base, () => executeSummarySave({
+      milestone_id: "M001",
+      artifact_type: "CONTEXT",
+      content: "# Context\n\nfinal content",
+    }, base));
+    assert.equal(unblocked.isError, undefined, "should not be blocked after depth verification");
+    assert.equal(unblocked.details.operation, "save_summary");
+  } finally {
+    if (originalEnv === undefined) {
+      delete process.env.GSD_PERSIST_WRITE_GATE_STATE;
+    } else {
+      process.env.GSD_PERSIST_WRITE_GATE_STATE = originalEnv;
+    }
+    clearDiscussionFlowState();
+    closeDatabase();
+    cleanup(base);
+  }
+});

package/src/resources/extensions/gsd/tests/worktree-db.test.ts

@@ -10,6 +10,8 @@ import {
   insertDecision,
   insertRequirement,
   insertArtifact,
+  insertMilestone,
+  getMilestone,
   getDecisionById,
   getRequirementById,
   _getAdapter,
@@ -442,4 +444,37 @@ console.log('\n=== worktree-db: reconcileWorktreeDb ===');
   cleanup(mainDir, wtDir);
 }
 
+// Test: reconcileWorktreeDb must NOT downgrade milestone status complete→active (#4372)
+{
+  const mainDir = tempDir();
+  const wtDir = tempDir();
+  const mainDb = path.join(mainDir, 'gsd.db');
+  const wtDb = path.join(wtDir, 'gsd.db');
+
+  // Seed main with a milestone already marked complete
+  seedMainDb(mainDb);
+  const mainAdapter = _getAdapter()!;
+  insertMilestone({ id: 'M-COMP', title: 'Completed Milestone', status: 'complete' });
+  // Manually mark completed_at so it's a realistic complete record
+  mainAdapter.prepare(`UPDATE milestones SET completed_at = '2025-06-01T00:00:00.000Z' WHERE id = 'M-COMP'`).run();
+  closeDatabase();
+
+  // Copy to worktree — the worktree has the milestone as 'active' (stale / older snapshot)
+  copyWorktreeDb(mainDb, wtDb);
+  openDatabase(wtDb);
+  const wtAdapter = _getAdapter()!;
+  wtAdapter.prepare(`UPDATE milestones SET status = 'active', completed_at = NULL WHERE id = 'M-COMP'`).run();
+  closeDatabase();
+
+  // Reconcile: main should win and keep 'complete'
+  openDatabase(mainDb);
+  reconcileWorktreeDb(mainDb, wtDb);
+
+  const m = getMilestone('M-COMP');
+  assert.ok(m !== null, 'milestone M-COMP still exists after reconcile');
+  assert.strictEqual(m!.status, 'complete', 'complete milestone must not be downgraded to active by stale worktree');
+
+  cleanup(mainDir, wtDir);
+}
+
 // ─── Final Report ──────────────────────────────────────────────────────────

package/src/resources/extensions/gsd/tests/worktree-journal-events.test.ts

@@ -190,7 +190,12 @@ describe("worktree journal events", () => {
     });
     const resolver = new WorktreeResolver(s, deps);
 
-    resolver.mergeAndExit("M001", makeNotifyCtx());
+    // Since #4380, mergeAndExit re-throws all errors after emitting the journal
+    // event and restoring state — callers must handle the throw.
+    assert.throws(
+      () => resolver.mergeAndExit("M001", makeNotifyCtx()),
+      /conflict in main/,
+    );
 
     const entries = readJournalEntries(tmp);
     const failed = entries.find(e => e.eventType === "worktree-merge-failed");

package/src/resources/extensions/gsd/tests/worktree-resolver.test.ts

@@ -313,6 +313,43 @@ test("enterMilestone uses originalBasePath as base for worktree ops", () => {
   assert.equal(createdFrom, "/project"); // uses originalBasePath, not current basePath
 });
 
+test("enterMilestone does not create double-nested worktree when originalBasePath is empty and basePath is a worktree path", () => {
+  // Regression test for #3729: when s.originalBasePath is "" (falsy) and
+  // s.basePath is already a worktree path, the expression
+  // `this.s.originalBasePath || this.s.basePath` evaluates to the worktree
+  // path. Passing that to createAutoWorktree produces a doubly-nested path
+  // like /project/.gsd/worktrees/M001/.gsd/worktrees/M002.
+  const wtPath = "/project/.gsd/worktrees/M001";
+  const s = makeSession({
+    basePath: wtPath,
+    originalBasePath: "/project", // will be overwritten below to simulate the bug
+  });
+  // Simulate the real bug: originalBasePath is "" (falsy) as it is when AutoSession
+  // is constructed fresh or reset() is called without auto-start re-setting it.
+  s.originalBasePath = "";
+
+  let createdFromPath = "";
+  const deps = makeDeps({
+    getAutoWorktreePath: () => null,
+    createAutoWorktree: (basePath: string, _mid: string) => {
+      createdFromPath = basePath;
+      return `/project/.gsd/worktrees/M002`;
+    },
+  });
+  const ctx = makeNotifyCtx();
+  const resolver = new WorktreeResolver(s, deps);
+
+  resolver.enterMilestone("M002", ctx);
+
+  // The path passed to createAutoWorktree must be the project root, NOT the
+  // worktree path. If it equals wtPath the worktree would be created at
+  // /project/.gsd/worktrees/M001/.gsd/worktrees/M002 (double-nesting).
+  assert.ok(
+    !createdFromPath.includes("/.gsd/worktrees/"),
+    `createAutoWorktree must be called with project root, got: "${createdFromPath}"`,
+  );
+});
+
 // ─── enterMilestone Tests (branch mode) ──────────────────────────────────────
 
 test("enterMilestone in branch mode calls enterBranchModeForMilestone and rebuilds GitService", () => {
@@ -577,9 +614,11 @@ test("mergeAndExit in worktree mode restores to project root on merge failure",
   const ctx = makeNotifyCtx();
   const resolver = new WorktreeResolver(s, deps);
 
-  resolver.mergeAndExit("M001", ctx);
+  // Error propagates (#4380) — callers handle recovery. restoreToProjectRoot()
+  // still runs before re-throw so state is consistent for the caller.
+  assert.throws(() => resolver.mergeAndExit("M001", ctx), /conflict in main/);
 
-  assert.equal(s.basePath, "/project"); // error recovery — restored
+  assert.equal(s.basePath, "/project"); // error recovery — restored before re-throw
   assert.ok(
     ctx.messages.some(
       (m) => m.level === "warning" && m.msg.includes("conflict in main"),
@@ -607,7 +646,8 @@ test("mergeAndExit failure message tells user worktree and branch are preserved
   const ctx = makeNotifyCtx();
   const resolver = new WorktreeResolver(s, deps);
 
-  resolver.mergeAndExit("M001", ctx);
+  // Error propagates (#4380) — notification is still emitted before re-throw
+  assert.throws(() => resolver.mergeAndExit("M001", ctx), /pathspec 'main' did not match/);
 
   const warning = ctx.messages.find((m) => m.level === "warning");
   assert.ok(warning, "a warning message is emitted");
@@ -643,7 +683,8 @@ test("mergeAndExit failure message references /gsd dispatch complete-milestone,
   const ctx = makeNotifyCtx();
   const resolver = new WorktreeResolver(s, deps);
 
-  resolver.mergeAndExit("M001", ctx);
+  // Error propagates (#4380) — notification is still emitted before re-throw
+  assert.throws(() => resolver.mergeAndExit("M001", ctx), /dirty working tree/);
 
   const warning = ctx.messages.find((m) => m.level === "warning");
   assert.ok(warning, "a warning message is emitted");
@@ -709,7 +750,8 @@ test("mergeAndExit in branch mode handles merge failure gracefully", () => {
   const ctx = makeNotifyCtx();
   const resolver = new WorktreeResolver(s, deps);
 
-  resolver.mergeAndExit("M001", ctx);
+  // Error propagates (#4380) — notification is still emitted before re-throw
+  assert.throws(() => resolver.mergeAndExit("M001", ctx), /branch merge conflict/);
 
   assert.ok(
     ctx.messages.some(
@@ -1069,3 +1111,34 @@ test("mergeAndExit in none mode remains a no-op when NOT in a worktree (#2625)",
   assert.equal(findCalls(deps.calls, "mergeMilestoneToMain").length, 0,
     "must NOT merge when not in a worktree and mode is none");
 });
+
+// ─── #4380 — Non-MergeConflictError must not be swallowed ────────────────────
+
+test("mergeAndExit propagates non-MergeConflictError to caller (#4380)", () => {
+  // Regression test: previously the catch block in _mergeWorktreeMode only
+  // re-threw MergeConflictError. Permission errors, filesystem errors, and other
+  // non-conflict failures were swallowed silently, making broken states impossible
+  // to diagnose and preventing callers (phases.ts) from applying their own
+  // error-recovery logic.
+  const permissionError = new Error("EACCES: permission denied, open '/project/.git/SQUASH_MSG'");
+  const s = makeSession({
+    basePath: "/project/.gsd/worktrees/M001",
+    originalBasePath: "/project",
+  });
+  const deps = makeDeps({
+    isInAutoWorktree: () => true,
+    getIsolationMode: () => "worktree",
+    mergeMilestoneToMain: () => {
+      throw permissionError;
+    },
+  });
+  const ctx = makeNotifyCtx();
+  const resolver = new WorktreeResolver(s, deps);
+
+  // The error must propagate — callers need it to apply their own recovery logic
+  assert.throws(
+    () => resolver.mergeAndExit("M001", ctx),
+    (err: unknown) => err === permissionError,
+    "non-MergeConflictError must propagate to the caller, not be swallowed",
+  );
+});

package/src/resources/extensions/gsd/tests/write-gate.test.ts

@@ -11,6 +11,10 @@
 
 import test from 'node:test';
 import assert from 'node:assert/strict';
+import { mkdirSync, writeFileSync, unlinkSync, existsSync, rmSync } from 'node:fs';
+import { join } from 'node:path';
+import { tmpdir } from 'node:os';
+import { randomUUID } from 'node:crypto';
 import {
   isDepthConfirmationAnswer,
   shouldBlockContextWrite,
@@ -20,8 +24,10 @@ import {
   markDepthVerified,
   isMilestoneDepthVerified,
   shouldBlockContextArtifactSave,
+  shouldBlockContextArtifactSaveInSnapshot,
   clearDiscussionFlowState,
   resetWriteGateState,
+  loadWriteGateSnapshot,
 } from '../bootstrap/write-gate.ts';
 
 // ─── Scenario 1: Blocks CONTEXT.md write during discussion without depth verification (absolute path) ──
@@ -488,3 +494,61 @@ test('write-gate: isDepthConfirmationAnswer falls back to (Recommended) match wi
     'should reject non-Recommended via fallback',
   );
 });
+
+// ─── Scenario 29: loadWriteGateSnapshot returns clean state when persist file deleted (#4343) ──
+
+test('write-gate: loadWriteGateSnapshot returns empty default when persist file is deleted (#4343)', () => {
+  const base = join(tmpdir(), `gsd-write-gate-4343-${randomUUID()}`);
+  mkdirSync(join(base, '.gsd', 'runtime'), { recursive: true });
+  const stateFilePath = join(base, '.gsd', 'runtime', 'write-gate-state.json');
+  const originalEnv = process.env.GSD_PERSIST_WRITE_GATE_STATE;
+
+  try {
+    process.env.GSD_PERSIST_WRITE_GATE_STATE = '1';
+
+    // Write a state file with a pending gate and verified milestone
+    writeFileSync(stateFilePath, JSON.stringify({
+      verifiedDepthMilestones: ['M001'],
+      activeQueuePhase: false,
+      pendingGateId: 'depth_verification_M001',
+    }));
+    assert.ok(existsSync(stateFilePath), 'precondition: state file exists');
+
+    // While file exists, snapshot reflects its contents
+    const beforeDeletion = loadWriteGateSnapshot(base);
+    assert.strictEqual(beforeDeletion.pendingGateId, 'depth_verification_M001', 'pending gate from file');
+    assert.deepEqual(beforeDeletion.verifiedDepthMilestones, ['M001'], 'verified milestones from file');
+
+    // User deletes the state file to clear the HARD BLOCK
+    unlinkSync(stateFilePath);
+    assert.ok(!existsSync(stateFilePath), 'state file deleted');
+
+    // After deletion in persist mode, snapshot should be clean (not stale in-memory)
+    const afterDeletion = loadWriteGateSnapshot(base);
+    assert.strictEqual(afterDeletion.pendingGateId, null, 'pendingGateId cleared after file deletion');
+    assert.deepEqual(afterDeletion.verifiedDepthMilestones, [], 'verifiedDepthMilestones cleared after file deletion');
+    assert.strictEqual(afterDeletion.activeQueuePhase, false, 'activeQueuePhase cleared after file deletion');
+
+    // The CONTEXT artifact block check must also resolve to unblocked after deletion+verification
+    // (simulate the re-verify flow users would do: delete → depth verify → save)
+    const stillBlocked = shouldBlockContextArtifactSaveInSnapshot(afterDeletion, 'CONTEXT', 'M001', null);
+    assert.strictEqual(stillBlocked.block, true, 'still blocked without new depth verification');
+
+    const verifiedSnapshot = {
+      ...afterDeletion,
+      verifiedDepthMilestones: ['M001'],
+    };
+    const unblocked = shouldBlockContextArtifactSaveInSnapshot(verifiedSnapshot, 'CONTEXT', 'M001', null);
+    assert.strictEqual(unblocked.block, false, 'unblocked after fresh depth verification');
+  } finally {
+    if (originalEnv === undefined) {
+      delete process.env.GSD_PERSIST_WRITE_GATE_STATE;
+    } else {
+      process.env.GSD_PERSIST_WRITE_GATE_STATE = originalEnv;
+    }
+    clearDiscussionFlowState();
+    try {
+      rmSync(base, { recursive: true, force: true });
+    } catch { /* swallow */ }
+  }
+});

package/src/resources/extensions/gsd/token-counter.ts

@@ -22,7 +22,11 @@ async function getEncoder(): Promise<TokenEncoder | null> {
 	try {
 		// @ts-ignore — tiktoken may not have type declarations in extensions tsconfig
 		const tiktoken = await import("tiktoken");
-		encoder = tiktoken.encoding_for_model("gpt-4o") as TokenEncoder;
+		// Use cl100k_base — the most conservative and broadly compatible BPE encoding.
+		// It is shared by GPT-3.5/GPT-4 and gives a safer (larger) estimate than
+		// gpt-4o's o200k_base encoding, which produces fewer tokens for the same text
+		// and would cause context windows for non-OpenAI providers to be under-counted.
+		encoder = tiktoken.get_encoding("cl100k_base") as TokenEncoder;
 		return encoder;
 	} catch {
 		encoderFailed = true;
@@ -30,20 +34,33 @@ async function getEncoder(): Promise<TokenEncoder | null> {
 	}
 }
 
-export async function countTokens(text: string): Promise<number> {
+/**
+ * Count tokens in `text` using tiktoken (cl100k_base) when available.
+ *
+ * When tiktoken is not loaded, falls back to a provider-aware character-ratio
+ * estimate via `estimateTokensForProvider`. Passing `provider` is recommended
+ * so the heuristic fallback is as accurate as possible.
+ */
+export async function countTokens(text: string, provider?: TokenProvider): Promise<number> {
 	const enc = await getEncoder();
 	if (enc) {
 		const tokens = enc.encode(text);
 		return tokens.length;
 	}
-	return Math.ceil(text.length / 4);
+	return estimateTokensForProvider(text, provider ?? "unknown");
 }
 
-export function countTokensSync(text: string): number {
+/**
+ * Synchronous token count — only accurate after `initTokenCounter()` resolves.
+ *
+ * Before init, or when tiktoken is unavailable, falls back to a provider-aware
+ * character-ratio estimate. Passing `provider` is recommended.
+ */
+export function countTokensSync(text: string, provider?: TokenProvider): number {
 	if (encoder) {
 		return encoder.encode(text).length;
 	}
-	return Math.ceil(text.length / 4);
+	return estimateTokensForProvider(text, provider ?? "unknown");
 }
 
 export async function initTokenCounter(): Promise<boolean> {

package/src/resources/extensions/gsd/tools/complete-milestone.ts

@@ -7,7 +7,7 @@
  */
 
 import { join } from "node:path";
-import { mkdirSync } from "node:fs";
+import { mkdirSync, existsSync } from "node:fs";
 
 import {
   transaction,
@@ -202,14 +202,20 @@ export async function handleCompleteMilestone(
     summaryPath = join(manualDir, `${params.milestoneId}-SUMMARY.md`);
   }
 
-  try {
-    await saveFile(summaryPath, summaryMd);
-  } catch (renderErr) {
-    // Disk render failed — roll back DB status so state stays consistent
-    logWarning("tool", `complete_milestone — disk render failed, rolling back DB status: ${(renderErr as Error).message}`);
-    updateMilestoneStatus(params.milestoneId, 'active', null);
-    invalidateStateCache();
-    return { error: `disk render failed: ${(renderErr as Error).message}` };
+  // Guard (#4598): if SUMMARY.md already exists on disk, do not overwrite it.
+  // This handles re-dispatch scenarios (DB/disk state divergence) where a prior
+  // completion already wrote the file. Overwriting would silently destroy the
+  // richer content the agent produced during the original completion run.
+  if (!existsSync(summaryPath)) {
+    try {
+      await saveFile(summaryPath, summaryMd);
+    } catch (renderErr) {
+      // Disk render failed — roll back DB status so state stays consistent
+      logWarning("tool", `complete_milestone — disk render failed, rolling back DB status: ${(renderErr as Error).message}`);
+      updateMilestoneStatus(params.milestoneId, 'active', null);
+      invalidateStateCache();
+      return { error: `disk render failed: ${(renderErr as Error).message}` };
+    }
   }
 
   // Invalidate all caches

package/src/resources/extensions/gsd/uok/plan-v2.ts

@@ -38,6 +38,29 @@ function hasFileContent(path: string | null): boolean {
   }
 }
 
+function getArtifactLookupBases(basePath: string): string[] {
+  const bases = [basePath];
+  const projectRoot = process.env.GSD_PROJECT_ROOT;
+  if (projectRoot && projectRoot.trim().length > 0 && projectRoot !== basePath) {
+    bases.push(projectRoot);
+  }
+  return bases;
+}
+
+function hasMilestoneFileContent(
+  basePath: string,
+  milestoneId: string,
+  suffix: string,
+): boolean {
+  const bases = getArtifactLookupBases(basePath);
+  for (const candidateBase of bases) {
+    if (hasFileContent(resolveMilestoneFile(candidateBase, milestoneId, suffix))) {
+      return true;
+    }
+  }
+  return false;
+}
+
 function countSliceResearchArtifacts(basePath: string, milestoneId: string, slices: SliceRow[]): number {
   let count = 0;
   for (const slice of slices) {
@@ -60,9 +83,9 @@ export function compileUnitGraphFromState(basePath: string, state: GSDState): Pl
   const slices = getMilestoneSlices(mid).sort((a, b) => Number(a.sequence ?? 0) - Number(b.sequence ?? 0));
   const nodes: UokGraphNode[] = [];
   const clarifyRoundLimit = PLAN_V2_CLARIFY_ROUND_LIMIT;
-  const draftContextIncluded = hasFileContent(resolveMilestoneFile(basePath, mid, "CONTEXT-DRAFT"));
-  const finalizedContextIncluded = hasFileContent(resolveMilestoneFile(basePath, mid, "CONTEXT"));
-  const researchSynthesized = hasFileContent(resolveMilestoneFile(basePath, mid, "RESEARCH"))
+  const draftContextIncluded = hasMilestoneFileContent(basePath, mid, "CONTEXT-DRAFT");
+  const finalizedContextIncluded = hasMilestoneFileContent(basePath, mid, "CONTEXT");
+  const researchSynthesized = hasMilestoneFileContent(basePath, mid, "RESEARCH")
     || countSliceResearchArtifacts(basePath, mid, slices) > 0;
 
   if (isExecutionEntryPhase(state.phase) && !finalizedContextIncluded) {

package/src/resources/extensions/gsd/workflow-logger.ts

@@ -58,7 +58,8 @@ export type LogComponent =
   | "memory-embeddings" // Memory layer embedding generation
   | "memory-ingest"     // Memory layer ingestion pipeline
   | "memory-backfill"   // ADR-013: decisions->memories backfill
-  | "context-mode";    // Context-mode exec sandbox and compaction snapshot
+  | "context-mode"     // Context-mode exec sandbox and compaction snapshot
+  | "preflight";       // Clean-root preflight gate at milestone completion
 
 export interface LogEntry {
   ts: string;

package/src/resources/extensions/gsd/worktree-resolver.ts

@@ -79,6 +79,35 @@ export interface NotifyCtx {
   ) => void;
 }
 
+// ─── Path Helpers ──────────────────────────────────────────────────────────
+
+/**
+ * Worktree marker segment — present in any path produced by worktreePath().
+ * Used to strip the worktree suffix and recover the project root (#3729).
+ */
+const WORKTREE_MARKER = "/.gsd/worktrees/";
+
+/**
+ * Resolve the project root from session path state.
+ *
+ * Prefers `originalBasePath` (always the project root when set), but falls
+ * back to `basePath` when `originalBasePath` is falsy (e.g. fresh AutoSession
+ * with default empty string). If `basePath` itself is inside a worktree
+ * directory (contains `/.gsd/worktrees/`), strip that suffix to recover the
+ * actual project root — preventing double-nested worktree paths (#3729).
+ */
+export function resolveProjectRoot(
+  originalBasePath: string,
+  basePath: string,
+): string {
+  let resolved = originalBasePath || basePath;
+  const markerIdx = resolved.indexOf(WORKTREE_MARKER);
+  if (markerIdx !== -1) {
+    resolved = resolved.slice(0, markerIdx);
+  }
+  return resolved;
+}
+
 // ─── WorktreeResolver ──────────────────────────────────────────────────────
 
 export class WorktreeResolver {
@@ -99,12 +128,12 @@ export class WorktreeResolver {
 
   /** Original project root — always the non-worktree path. */
   get projectRoot(): string {
-    return this.s.originalBasePath || this.s.basePath;
+    return resolveProjectRoot(this.s.originalBasePath, this.s.basePath);
   }
 
   /** Path for auto.lock file — same as the old lockBase(). */
   get lockPath(): string {
-    return this.s.originalBasePath || this.s.basePath;
+    return resolveProjectRoot(this.s.originalBasePath, this.s.basePath);
   }
 
   // ── Private Helpers ────────────────────────────────────────────────────
@@ -182,7 +211,10 @@ export class WorktreeResolver {
       return;
     }
 
-    const basePath = this.s.originalBasePath || this.s.basePath;
+    // Resolve the project root for worktree operations via shared helper.
+    // Handles the case where originalBasePath is falsy and basePath is itself
+    // a worktree path — prevents double-nested worktree paths (#3729).
+    const basePath = resolveProjectRoot(this.s.originalBasePath, this.s.basePath);
     debugLog("WorktreeResolver", {
       action: "enterMilestone",
       milestoneId,
@@ -569,11 +601,13 @@ export class WorktreeResolver {
         }
       }
 
-      // Re-throw MergeConflictError so the auto loop can detect real code
-      // conflicts and stop instead of retrying forever (#2330).
-      if (err instanceof MergeConflictError) {
-        throw err;
-      }
+      // Restore state before re-throwing so callers always get a consistent
+      // session (#4380).
+      this.restoreToProjectRoot();
+      // Re-throw: MergeConflictError stops the auto loop (#2330); non-conflict
+      // errors (permission denied, filesystem failures) must also propagate so
+      // broken states are diagnosable (#4380).
+      throw err;
     }
 
     // Always restore basePath and rebuild — whether merge succeeded or failed
@@ -659,6 +693,8 @@ export class WorktreeResolver {
         error: msg,
       });
       ctx.notify(`Milestone merge failed (branch mode): ${msg}`, "warning");
+      // Re-throw all errors so callers can apply their own recovery logic (#4380).
+      throw err;
     }
   }
 
@@ -681,7 +717,16 @@ export class WorktreeResolver {
       currentMilestoneId,
       nextMilestoneId,
     });
-    this.mergeAndExit(currentMilestoneId, ctx);
+    try {
+      this.mergeAndExit(currentMilestoneId, ctx);
+    } catch (err) {
+      // mergeAndExit emits a warning and restores state when it fails during
+      // merge/cleanup. But if it throws before recovery runs (e.g., in
+      // validateMilestoneId or emitJournalEvent), basePath won't be restored
+      // to projectRoot — re-throw so we don't enter the next milestone with
+      // the current one unmerged.
+      if (this.s.basePath !== this.projectRoot) throw err;
+    }
     this.enterMilestone(nextMilestoneId, ctx);
   }
 }

package/src/resources/extensions/mcp-client/index.ts

@@ -514,7 +514,7 @@ export default function (pi: ExtensionAPI) {
 		await closeAll();
 	});
 
-	pi.on("session_switch", async () => {
+	pi.on("session_before_switch", async () => {
 		await closeAll();
 		configCache = null;
 	});

package/src/resources/extensions/ollama/index.ts

@@ -16,7 +16,8 @@
  * Respects OLLAMA_HOST env var for non-default endpoints.
  */
 
-import { importExtensionModule, type ExtensionAPI } from "@gsd/pi-coding-agent";
+import { type ExtensionAPI } from "@gsd/pi-coding-agent";
+import { importExtensionModule } from "@gsd/pi-coding-agent";
 import * as client from "./ollama-client.js";
 import { discoverModels } from "./ollama-discovery.js";
 import { registerOllamaCommands } from "./ollama-commands.js";
@@ -73,12 +74,11 @@ async function probeAndRegister(pi: ExtensionAPI): Promise<boolean> {
 	// so the "ollama" fallback is harmless. For cloud endpoints (OLLAMA_HOST pointing
 	// to ollama.com or a remote instance), OLLAMA_API_KEY is picked up here.
 	pi.registerProvider("ollama", {
-		authMode: "apiKey",
+		// authMode and isReady removed from ProviderConfig in pi 0.67.2
 		apiKey: process.env.OLLAMA_API_KEY ?? "ollama",
 		baseUrl,
 		api: "ollama-chat",
 		streamSimple: streamOllamaChat,
-		isReady: () => true,
 		models: models.map((m) => ({
 			id: m.id,
 			name: m.name,