@opengsd/gsd-pi 1.9.0-dev.d2070876 → 1.9.0-dev.e10b60d4

package/src/resources/extensions/gsd/flat-phase-migration.ts

@@ -155,19 +155,6 @@ function isInsideFlatProjectionBackup(backupDir: string, src: string): boolean {
   return src === phaseBackupDir || src.startsWith(`${phaseBackupDir}/`) || src.startsWith(`${phaseBackupDir}\\`);
 }
 
-function removeFlatProjectionBackup(backupDir: string): void {
-  const phaseBackupDir = join(backupDir, "__phases");
-  if (!existsSync(phaseBackupDir)) return;
-  try {
-    removePathWithRetries(phaseBackupDir);
-  } catch (err) {
-    logWarning(
-      "migration",
-      `flat-phase migration succeeded but could not remove temporary ${LAYOUT_SEGMENTS.level1}/ backup: ${(err as Error).message}`,
-    );
-  }
-}
-
 function restoreFlatProjectionFromBackup(basePath: string, backupDir: string): void {
   const phaseBackupDir = join(backupDir, "__phases");
   if (!existsSync(phaseBackupDir)) return;
@@ -507,5 +494,4 @@ export async function migrateToFlatPhase(basePath: string): Promise<void> {
       `flat-phase migration succeeded but could not remove ${LEGACY_MIGRATING_SEGMENT}: ${(err as Error).message}`,
     );
   }
-  removeFlatProjectionBackup(backupDir);
 }

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

@@ -67,13 +67,6 @@ export type { SliceRow, TaskRow } from "./db-task-slice-rows.js";
 
 import { TERMINAL_STATUS_SQL } from "./db/sql-constants.js";
 import { applyStatusTransition } from "./db/writers/status.js";
-import {
-  LAYOUT_SEGMENTS,
-  derivePhaseSlug,
-  milestoneIdToPhaseNum,
-  milestoneIdUniqueSuffix,
-  phaseDirName,
-} from "./layout-policy.js";
 
 export function insertDecision(d: Omit<Decision, "seq">): void {
   if (!getDbOrNull()!) throw new GSDError(GSD_STALE_STATE, "gsd-db: No database open");
@@ -213,47 +206,6 @@ export function insertArtifact(a: {
   });
 }
 
-function canonicalPhaseDirNameForDb(milestoneId: string, title: string): string {
-  const phaseNum = milestoneIdToPhaseNum(milestoneId);
-  const slug = derivePhaseSlug(title || milestoneId);
-  const suffix = milestoneIdUniqueSuffix(milestoneId);
-  return phaseDirName(phaseNum, suffix ? `${suffix}-${slug}` : slug);
-}
-
-function reconcileMilestonePhaseArtifactPaths(milestoneId: string, title: string): void {
-  const db = getDbOrNull()!;
-  const phaseNumPrefix = String(milestoneIdToPhaseNum(milestoneId)).padStart(2, "0");
-  const canonicalDir = canonicalPhaseDirNameForDb(milestoneId, title);
-  const staleRows = db.prepare(
-    `SELECT path
-       FROM artifacts
-      WHERE milestone_id = :milestone_id
-        AND path LIKE :phase_prefix`,
-  ).all({
-    ":milestone_id": milestoneId,
-    ":phase_prefix": `${LAYOUT_SEGMENTS.level1}/${phaseNumPrefix}-%/%`,
-  }) as Array<{ path: string }>;
-
-  const updatePath = db.prepare("UPDATE artifacts SET path = :new_path WHERE path = :old_path");
-  const deletePath = db.prepare("DELETE FROM artifacts WHERE path = :path");
-  const existingPath = db.prepare("SELECT 1 AS present FROM artifacts WHERE path = :path");
-
-  for (const row of staleRows) {
-    const parts = row.path.split("/");
-    if (parts.length < 3) continue;
-    if (parts[0] !== LAYOUT_SEGMENTS.level1) continue;
-    if (parts[1] === canonicalDir) continue;
-    if (!parts[1]?.startsWith(`${phaseNumPrefix}-`)) continue;
-
-    const newPath = [LAYOUT_SEGMENTS.level1, canonicalDir, ...parts.slice(2)].join("/");
-    if (existingPath.get({ ":path": newPath })) {
-      deletePath.run({ ":path": row.path });
-      continue;
-    }
-    updatePath.run({ ":new_path": newPath, ":old_path": row.path });
-  }
-}
-
 export interface MilestonePlanningRecord {
   vision: string;
   successCriteria: string[];
@@ -335,43 +287,39 @@ export function insertMilestone(m: {
 
 export function upsertMilestonePlanning(milestoneId: string, planning: Partial<MilestonePlanningRecord> & { title?: string; status?: string; depends_on?: string[] }): void {
   if (!getDbOrNull()!) throw new GSDError(GSD_STALE_STATE, "gsd-db: No database open");
-  transaction(() => {
-    getDbOrNull()!.prepare(
-      `UPDATE milestones SET
-        title = COALESCE(NULLIF(:title, ''), title),
-        status = COALESCE(NULLIF(:status, ''), status),
-        depends_on = COALESCE(:depends_on, depends_on),
-        vision = COALESCE(:vision, vision),
-        success_criteria = COALESCE(:success_criteria, success_criteria),
-        key_risks = COALESCE(:key_risks, key_risks),
-        proof_strategy = COALESCE(:proof_strategy, proof_strategy),
-        verification_contract = COALESCE(:verification_contract, verification_contract),
-        verification_integration = COALESCE(:verification_integration, verification_integration),
-        verification_operational = COALESCE(:verification_operational, verification_operational),
-        verification_uat = COALESCE(:verification_uat, verification_uat),
-        definition_of_done = COALESCE(:definition_of_done, definition_of_done),
-        requirement_coverage = COALESCE(:requirement_coverage, requirement_coverage),
-        boundary_map_markdown = COALESCE(:boundary_map_markdown, boundary_map_markdown)
-       WHERE id = :id`,
-    ).run({
-      ":id": milestoneId,
-      ":title": planning.title ?? "",
-      ":status": planning.status ?? "",
-      ":depends_on": planning.depends_on ? JSON.stringify(planning.depends_on) : null,
-      ":vision": planning.vision ?? null,
-      ":success_criteria": planning.successCriteria ? JSON.stringify(planning.successCriteria) : null,
-      ":key_risks": planning.keyRisks ? JSON.stringify(planning.keyRisks) : null,
-      ":proof_strategy": planning.proofStrategy ? JSON.stringify(planning.proofStrategy) : null,
-      ":verification_contract": planning.verificationContract ?? null,
-      ":verification_integration": planning.verificationIntegration ?? null,
-      ":verification_operational": planning.verificationOperational ?? null,
-      ":verification_uat": planning.verificationUat ?? null,
-      ":definition_of_done": planning.definitionOfDone ? JSON.stringify(planning.definitionOfDone) : null,
-      ":requirement_coverage": planning.requirementCoverage ?? null,
-      ":boundary_map_markdown": planning.boundaryMapMarkdown ?? null,
-    });
-    const finalTitle = planning.title?.trim();
-    if (finalTitle) reconcileMilestonePhaseArtifactPaths(milestoneId, finalTitle);
+  getDbOrNull()!.prepare(
+    `UPDATE milestones SET
+      title = COALESCE(NULLIF(:title, ''), title),
+      status = COALESCE(NULLIF(:status, ''), status),
+      depends_on = COALESCE(:depends_on, depends_on),
+      vision = COALESCE(:vision, vision),
+      success_criteria = COALESCE(:success_criteria, success_criteria),
+      key_risks = COALESCE(:key_risks, key_risks),
+      proof_strategy = COALESCE(:proof_strategy, proof_strategy),
+      verification_contract = COALESCE(:verification_contract, verification_contract),
+      verification_integration = COALESCE(:verification_integration, verification_integration),
+      verification_operational = COALESCE(:verification_operational, verification_operational),
+      verification_uat = COALESCE(:verification_uat, verification_uat),
+      definition_of_done = COALESCE(:definition_of_done, definition_of_done),
+      requirement_coverage = COALESCE(:requirement_coverage, requirement_coverage),
+      boundary_map_markdown = COALESCE(:boundary_map_markdown, boundary_map_markdown)
+     WHERE id = :id`,
+  ).run({
+    ":id": milestoneId,
+    ":title": planning.title ?? "",
+    ":status": planning.status ?? "",
+    ":depends_on": planning.depends_on ? JSON.stringify(planning.depends_on) : null,
+    ":vision": planning.vision ?? null,
+    ":success_criteria": planning.successCriteria ? JSON.stringify(planning.successCriteria) : null,
+    ":key_risks": planning.keyRisks ? JSON.stringify(planning.keyRisks) : null,
+    ":proof_strategy": planning.proofStrategy ? JSON.stringify(planning.proofStrategy) : null,
+    ":verification_contract": planning.verificationContract ?? null,
+    ":verification_integration": planning.verificationIntegration ?? null,
+    ":verification_operational": planning.verificationOperational ?? null,
+    ":verification_uat": planning.verificationUat ?? null,
+    ":definition_of_done": planning.definitionOfDone ? JSON.stringify(planning.definitionOfDone) : null,
+    ":requirement_coverage": planning.requirementCoverage ?? null,
+    ":boundary_map_markdown": planning.boundaryMapMarkdown ?? null,
   });
 }
 

package/src/resources/extensions/gsd/tests/auto-loop.test.ts

@@ -41,7 +41,6 @@ import { claimMilestoneLease } from "../db/milestone-leases.js";
 import { recordDispatchClaim, markCanceled } from "../db/unit-dispatches.js";
 import { setRuntimeKv, getRuntimeKv } from "../db/runtime-kv.js";
 import { SourceObservationStore } from "../source-observations.js";
-import { autoCommitCurrentBranch } from "../worktree.js";
 
 // ─── Helpers ─────────────────────────────────────────────────────────────────
 
@@ -833,37 +832,6 @@ test("runUnit returns cancelled when session creation fails", async () => {
   assert.equal(pi.calls.length, 0);
 });
 
-test("runUnit returns cancelled when command context lacks newSession", async () => {
-  _resetPendingResolve();
-
-  const ctx = {
-    ...makeMockCtx(),
-    ui: {
-      notify: () => {},
-      setStatus: () => {},
-      setWorkingMessage: () => {},
-    },
-    sessionManager: {
-      getEntries: () => [],
-    },
-    modelRegistry: {
-      getProviderAuthMode: () => undefined,
-      isProviderRequestReady: () => true,
-    },
-  } as any;
-  const pi = makeMockPi();
-  const s = makeMockSession();
-  s.cmdCtx = {} as any;
-
-  const result = await runUnit(ctx, pi, s, "task", "T01", "prompt");
-
-  assert.equal(result.status, "cancelled");
-  assert.equal(result.errorContext?.category, "session-failed");
-  assert.equal(result.errorContext?.isTransient, false);
-  assert.match(result.errorContext?.message ?? "", /missing newSession/);
-  assert.equal(pi.calls.length, 0);
-});
-
 test("runUnit: TypeError from newSession is classified as structural (isTransient: false)", async () => {
   // Regression for #572: a TypeError thrown from newSession (e.g. "something is
   // not a function") indicates a programming error, not a transient provider
@@ -1614,130 +1582,6 @@ test("autoLoop exits when s.active is set to false", async (t) => {
   );
 });
 
-test("autoLoop stops before dispatch when command context lacks newSession", async () => {
-  _resetPendingResolve();
-
-  const ctx = makeMockCtx();
-  ctx.ui.setStatus = () => {};
-  const pi = makeMockPi();
-  const s = makeLoopSession({
-    cmdCtx: {
-      getContextUsage: () => ({ percent: 10, tokens: 1000, limit: 10000 }),
-    },
-  });
-  let stopReason: string | undefined;
-  let preserveWorktree: boolean | undefined;
-  let deriveCalled = false;
-
-  try {
-    const deps = makeMockDeps({
-      stopAuto: async (_ctx, _pi, reason, options) => {
-        stopReason = reason;
-        preserveWorktree = options?.preserveWorktree;
-        s.active = false;
-      },
-      deriveState: async () => {
-        deriveCalled = true;
-        throw new Error("deriveState should not run without command session support");
-      },
-    });
-
-    await autoLoop(ctx, pi, s, deps);
-
-    assert.equal(stopReason, "Auto-mode has no command context for dispatch.");
-    assert.equal(preserveWorktree, true);
-    assert.equal(deriveCalled, false);
-    assert.equal(pi.calls.length, 0);
-  } finally {
-    rmSync(s.basePath, { recursive: true, force: true });
-  }
-});
-
-test("autoLoop commits open unit work when command context lacks newSession", async () => {
-  _resetPendingResolve();
-
-  const ctx = makeMockCtx();
-  ctx.ui.setStatus = () => {};
-  const pi = makeMockPi();
-  const s = makeLoopSession({
-    cmdCtx: {
-      getContextUsage: () => ({ percent: 10, tokens: 1000, limit: 10000 }),
-    },
-    currentUnit: { type: "execute-task", id: "T01", startedAt: Date.now() },
-  });
-  const outputPath = join(s.basePath, "executor-output.txt");
-  let autoCommitArgs: { unitType: string; unitId: string } | undefined;
-  let preserveWorktree: boolean | undefined;
-
-  try {
-    const deps = makeMockDeps({
-      autoCommitUnit: async (basePath, unitType, unitId) => {
-        autoCommitArgs = { unitType, unitId };
-        return autoCommitCurrentBranch(basePath, unitType, unitId);
-      },
-      stopAuto: async (_ctx, _pi, _reason, options) => {
-        preserveWorktree = options?.preserveWorktree;
-        s.active = false;
-      },
-      deriveState: async () => {
-        throw new Error("deriveState should not run without command session support");
-      },
-    });
-
-    writeFileSync(outputPath, "open unit work before stop\n", "utf-8");
-
-    await autoLoop(ctx, pi, s, deps);
-
-    assert.deepEqual(autoCommitArgs, { unitType: "execute-task", unitId: "T01" });
-    assert.equal(preserveWorktree, true);
-    const committed = execSync("git show HEAD:executor-output.txt", {
-      cwd: s.basePath,
-      encoding: "utf-8",
-    });
-    assert.equal(committed, "open unit work before stop\n");
-    assert.equal(pi.calls.length, 0);
-  } finally {
-    rmSync(s.basePath, { recursive: true, force: true });
-  }
-});
-
-test("autoLoop snapshots dirty work when unit dispatch crashes", async () => {
-  _resetPendingResolve();
-
-  const ctx = makeMockCtx();
-  ctx.ui.setStatus = () => {};
-  const pi = makeMockPi();
-  const s = makeLoopSession();
-  const outputPath = join(s.basePath, "executor-output.txt");
-  let autoCommitCalls = 0;
-
-  try {
-    const deps = makeMockDeps({
-      ensurePreconditions: () => {
-        writeFileSync(outputPath, "saved before crash\n", "utf-8");
-        throw new Error("dispatch crash after file write");
-      },
-      autoCommitUnit: async (basePath, unitType, unitId) => {
-        autoCommitCalls++;
-        const commitMsg = autoCommitCurrentBranch(basePath, unitType, unitId);
-        s.active = false;
-        return commitMsg;
-      },
-    });
-
-    await autoLoop(ctx, pi, s, deps);
-
-    assert.equal(autoCommitCalls, 1);
-    const committed = execSync("git show HEAD:executor-output.txt", {
-      cwd: s.basePath,
-      encoding: "utf-8",
-    });
-    assert.equal(committed, "saved before crash\n");
-  } finally {
-    rmSync(s.basePath, { recursive: true, force: true });
-  }
-});
-
 test("autoLoop pauses visibly when Auto Orchestration Module is not wired", async () => {
   _resetPendingResolve();
 

package/src/resources/extensions/gsd/tests/auto-start-index-lock.test.ts

@@ -4,7 +4,7 @@ import { existsSync, mkdtempSync, mkdirSync, rmSync, writeFileSync } from "node:
 import { join } from "node:path";
 import { tmpdir } from "node:os";
 
-import { hasGitIndexLockForTest, reconcileFlatPhaseBootstrapLayout } from "../auto-start.ts";
+import { hasGitIndexLockForTest } from "../auto-start.ts";
 
 test("bootstrapAutoSession detects .git/index.lock without deleting it", (t) => {
   const base = mkdtempSync(join(tmpdir(), "gsd-index-lock-"));
@@ -24,23 +24,3 @@ test("bootstrapAutoSession reports no index lock when the lock file is absent",
 
   assert.equal(hasGitIndexLockForTest(base), false);
 });
-
-test("bootstrapAutoSession removes empty legacy milestones dir in flat-phase projects", (t) => {
-  const base = mkdtempSync(join(tmpdir(), "gsd-flat-bootstrap-clean-"));
-  t.after(() => rmSync(base, { recursive: true, force: true }));
-  mkdirSync(join(base, ".gsd", "phases"), { recursive: true });
-  mkdirSync(join(base, ".gsd", "milestones"), { recursive: true });
-
-  assert.equal(reconcileFlatPhaseBootstrapLayout(base), true);
-  assert.equal(existsSync(join(base, ".gsd", "phases")), true);
-  assert.equal(existsSync(join(base, ".gsd", "milestones")), false);
-});
-
-test("bootstrapAutoSession creates phases instead of milestones for empty GSD state", (t) => {
-  const base = mkdtempSync(join(tmpdir(), "gsd-flat-bootstrap-init-"));
-  t.after(() => rmSync(base, { recursive: true, force: true }));
-
-  assert.equal(reconcileFlatPhaseBootstrapLayout(base), true);
-  assert.equal(existsSync(join(base, ".gsd", "phases")), true);
-  assert.equal(existsSync(join(base, ".gsd", "milestones")), false);
-});

package/src/resources/extensions/gsd/tests/auto-wrapup-inflight-guard.test.ts

@@ -3,8 +3,7 @@
 
 import { describe, test } from "node:test";
 import assert from "node:assert/strict";
-import { mkdtempSync, mkdirSync, realpathSync, rmSync, writeFileSync } from "node:fs";
-import { execSync } from "node:child_process";
+import { mkdtempSync, mkdirSync, realpathSync, rmSync } from "node:fs";
 import { join } from "node:path";
 import { tmpdir } from "node:os";
 
@@ -97,78 +96,6 @@ describe("hook dispatch session workspace root", () => {
     assert.equal(dispatched, true);
     assert.deepEqual(newSessionOptions, { workspaceRoot: basePath });
   });
-
-  test("dispatchHookUnit commits in-flight work when command context lacks newSession", async (t) => {
-    const originalCwd = process.cwd();
-    const basePath = realpathSync(mkdtempSync(join(tmpdir(), "gsd-hook-nosnap-")));
-    mkdirSync(join(basePath, ".gsd"), { recursive: true });
-    execSync("git init --initial-branch=main", { cwd: basePath, stdio: "ignore" });
-    execSync("git config user.email test@test.com", { cwd: basePath, stdio: "ignore" });
-    execSync("git config user.name Test", { cwd: basePath, stdio: "ignore" });
-    execSync("git commit --allow-empty -m init", { cwd: basePath, stdio: "ignore" });
-
-    autoSession.reset();
-    autoSession.active = true;
-    autoSession.basePath = basePath;
-    autoSession.originalBasePath = basePath;
-    // Simulate an in-flight unit whose executor already wrote files, then a hook
-    // fires with a command context missing newSession.
-    autoSession.currentUnit = {
-      type: "execute-task",
-      id: "M001/S01/T01",
-      startedAt: Date.now(),
-    };
-    t.after(() => {
-      try {
-        process.chdir(originalCwd);
-      } catch {
-        // best effort cleanup after cwd-sensitive dispatch tests
-      }
-      autoSession.reset();
-      rmSync(basePath, { recursive: true, force: true });
-    });
-
-    const outputPath = join(basePath, "executor-output.txt");
-    writeFileSync(outputPath, "in-flight executor work\n", "utf-8");
-
-    // Command context intentionally lacks newSession — the guard must snapshot
-    // the dirty work before stopping instead of discarding it.
-    const ctx = {
-      ui: {
-        notify: () => {},
-        setStatus: () => {},
-        setWidget: () => {},
-      },
-      modelRegistry: {
-        getAvailable: () => [],
-      },
-      sessionManager: {
-        getSessionFile: () => join(basePath, "session.jsonl"),
-      },
-    };
-    const pi = {
-      sendMessage: () => {},
-      setModel: async () => true,
-    };
-
-    const dispatched = await dispatchHookUnit(
-      ctx as any,
-      pi as any,
-      "review",
-      "execute-task",
-      "M001/S01/T01",
-      "review the completed unit",
-      undefined,
-      basePath,
-    );
-
-    assert.equal(dispatched, false);
-    const committed = execSync("git show HEAD:executor-output.txt", {
-      cwd: basePath,
-      encoding: "utf-8",
-    });
-    assert.equal(committed, "in-flight executor work\n");
-  });
 });
 
 describe("deep setup approval questions pause immediately", () => {

package/src/resources/extensions/gsd/tests/doctor-scope-db-unavailable.test.ts

@@ -167,45 +167,6 @@ test("checkEngineHealth keeps PLAN checkbox divergence after stale projection fl
   assert.match(readFileSync(plan.planPath, "utf-8"), /- \[ \] \*\*T01\*\*:/);
 });
 
-test("checkEngineHealth ignores stale suffixed flat-phase duplicate when bare milestone exists", async (t) => {
-  const base = mkdtempSync(join(tmpdir(), "gsd-doctor-checkbox-flat-duplicate-"));
-  t.after(() => rmSync(base, { recursive: true, force: true }));
-
-  const gsdDir = join(base, ".gsd");
-  mkdirSync(gsdDir, { recursive: true });
-
-  openDatabase(join(gsdDir, "gsd.db"));
-  insertMilestone({ id: "M003", title: "M003-vaz73w: New milestone M003-vaz73w", status: "active" });
-  insertSlice({ id: "S01", milestoneId: "M003", title: "Slice", status: "pending", risk: "low", depends: [], sequence: 1 });
-  for (const taskId of ["T01", "T02", "T03"]) {
-    insertTask({ id: taskId, milestoneId: "M003", sliceId: "S01", title: taskId, status: "complete", sequence: Number(taskId.slice(1)) });
-  }
-
-  insertMilestone({ id: "M003-vaz73w", title: "New milestone M003-vaz73w", status: "active" });
-  insertSlice({ id: "S01", milestoneId: "M003-vaz73w", title: "Slice", status: "pending", risk: "low", depends: [], sequence: 1 });
-  for (const taskId of ["T01", "T02", "T03"]) {
-    insertTask({ id: taskId, milestoneId: "M003-vaz73w", sliceId: "S01", title: taskId, status: "complete", sequence: Number(taskId.slice(1)) });
-  }
-
-  const canonicalPlan = await renderPlanFromDb(base, "M003", "S01");
-  const staleDir = join(gsdDir, "phases", "03-vaz73w-new-milestone-m003-vaz73w");
-  mkdirSync(staleDir, { recursive: true });
-  writeFileSync(
-    join(staleDir, "03-01-PLAN.md"),
-    canonicalPlan.content.replace("- [x] **T03**:", "- [ ] **T03**:"),
-    "utf-8",
-  );
-
-  const issues: any[] = [];
-  await checkEngineHealth(base, issues, []);
-
-  assert.deepEqual(
-    issues.filter((issue) => issue.code === "checkbox_db_status_divergence").map((issue) => issue.unitId),
-    [],
-    "stale suffixed duplicate phase projection must not compete with the bare milestone projection",
-  );
-});
-
 test("checkEngineHealth reads task checkboxes from the <tasks> block, not a stray line above it", async (t) => {
   const base = mkdtempSync(join(tmpdir(), "gsd-doctor-task-section-"));
   t.after(() => rmSync(base, { recursive: true, force: true }));
@@ -467,50 +428,6 @@ test("checkEngineHealth repair prunes stale phases artifact rows with present mi
   assert.deepEqual(rows.map((row) => row.path), []);
 });
 
-test("checkEngineHealth repair prunes stale phases artifact rows with renamed flat-phase files", async (t) => {
-  const base = mkdtempSync(join(tmpdir(), "gsd-doctor-prune-renamed-flat-phase-artifact-"));
-  t.after(() => rmSync(base, { recursive: true, force: true }));
-
-  const gsdDir = join(base, ".gsd");
-  const stalePath = "phases/01-new-milestone-m001/01-01-PLAN.md";
-  const replacementPath = "phases/01-lokably-brand-foundation-and-welcome-pag/01-01-PLAN.md";
-  mkdirSync(join(gsdDir, "phases", "01-lokably-brand-foundation-and-welcome-pag"), { recursive: true });
-  writeFileSync(join(gsdDir, replacementPath), "# Plan\n", "utf-8");
-
-  openDatabase(join(gsdDir, "gsd.db"));
-  insertArtifact({
-    path: stalePath,
-    artifact_type: "PLAN",
-    milestone_id: "M001",
-    slice_id: "S01",
-    task_id: null,
-    full_content: "# stale plan\n",
-  });
-
-  const beforeIssues: any[] = [];
-  await checkEngineHealth(base, beforeIssues, []);
-
-  const beforeIssue = beforeIssues.find((issue) => issue.code === "artifact_file_missing" && issue.file === stalePath);
-  assert.ok(beforeIssue, "stale renamed phases row should be reported when repair is off");
-  assert.equal(beforeIssue.fixable, true, "renamed phases rows with a flat replacement should be fixable");
-
-  const repairIssues: any[] = [];
-  const fixes: string[] = [];
-  await checkEngineHealth(base, repairIssues, fixes, { repair: true });
-
-  assert.equal(
-    repairIssues.some((issue) => issue.code === "artifact_file_missing" && issue.file === stalePath),
-    false,
-    "repair should not report stale rows it pruned",
-  );
-  assert.ok(fixes.includes(`pruned stale flat-phase artifact row ${stalePath}`));
-
-  const rows = _getAdapter()!
-    .prepare("SELECT path FROM artifacts ORDER BY path")
-    .all() as Array<{ path: string }>;
-  assert.deepEqual(rows.map((row) => row.path), []);
-});
-
 test("checkEngineHealth repair keeps phases rows whose own file is still present", async (t) => {
   const base = mkdtempSync(join(tmpdir(), "gsd-doctor-keep-present-phase-artifact-"));
   t.after(() => rmSync(base, { recursive: true, force: true }));

package/src/resources/extensions/gsd/tests/flat-phase-migration.test.ts

@@ -122,7 +122,7 @@ test("migrateToFlatPhase creates a backup", async () => {
   assert.ok(backups.length >= 1, "at least one migrate-* backup dir should exist");
 });
 
-test("migrateToFlatPhase removes disposable phases snapshot after successful migration", async () => {
+test("migrateToFlatPhase backs up existing phases projection before clearing it", async () => {
   const base = makeTmp();
   const reviewPath = join(base, ".gsd", "phases", "01-foundation", "PLAN-REVIEW.md");
   mkdirSync(join(base, ".gsd", "phases", "01-foundation"), { recursive: true });
@@ -133,10 +133,11 @@ test("migrateToFlatPhase removes disposable phases snapshot after successful mig
   const backupRoot = join(base, ".gsd-backups");
   const backups = readdirSync(backupRoot).filter(d => d.startsWith("migrate-"));
   assert.equal(backups.length, 1, "one migrate backup should exist");
+  const backedUpReview = join(backupRoot, backups[0]!, "__phases", "01-foundation", "PLAN-REVIEW.md");
   assert.equal(
-    existsSync(join(backupRoot, backups[0]!, "__phases")),
-    false,
-    "temporary phases/ recovery snapshot should be removed after success",
+    readFileSync(backedUpReview, "utf-8"),
+    "# Plan Review\n\nHand-authored review.",
+    "pre-existing phases/ files should have a recovery copy",
   );
 });
 
@@ -201,7 +202,7 @@ test("failed migration rolls back without leaking a .gsd-backups/migrate-* dir",
   assert.equal(leaked.length, 0, "rollback must delete the migrate-* backup it created");
 });
 
-test("resumed migration removes disposable phases snapshot after success", async () => {
+test("resumed migration stores phases backup in retained migrate snapshot", async () => {
   const base = makeTmp();
   const milestonesPath = join(base, ".gsd", "milestones");
   const migratingPath = join(base, ".gsd", "milestones.migrating");
@@ -217,9 +218,9 @@ test("resumed migration removes disposable phases snapshot after success", async
   const backups = readdirSync(backupRoot).filter((d) => d.startsWith("migrate-"));
   assert.equal(backups.length, 1, "resumed migration should create one retained migrate backup");
   assert.equal(
-    existsSync(join(backupRoot, backups[0]!, "__phases")),
-    false,
-    "temporary phases/ recovery snapshot should be removed after resumed success",
+    readFileSync(join(backupRoot, backups[0]!, "__phases", "01-foundation", "PLAN-REVIEW.md"), "utf-8"),
+    "# Plan Review\n\nResume recovery copy.",
+    "resume should retain the phases snapshot under .gsd-backups",
   );
   assert.equal(
     existsSync(join(migratingPath, "__phases")),

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

@@ -46,9 +46,6 @@ import {
   tryCreateMemoriesFts,
   _isLikelyWslDrvFsPathForTest,
   _shouldAttemptVacuumRecoveryForTest,
-  insertArtifact,
-  getArtifact,
-  upsertMilestonePlanning,
 } from '../gsd-db.ts';
 import { MigrationBackupError } from '../db-migration-backup.ts';
 import { _resetLogs, peekLogs, setStderrLoggingEnabled } from '../workflow-logger.ts';
@@ -360,35 +357,6 @@ describe('gsd-db', () => {
     closeDatabase();
   });
 
-  test("gsd-db: upsertMilestonePlanning rewrites placeholder phase artifact paths to final title slug", () => {
-    openDatabase(":memory:");
-
-    const stalePath = "phases/01-new-milestone-m001/01-ROADMAP.md";
-    const finalPath = "phases/01-lokably-brand-foundation-and-welcome-pag/01-ROADMAP.md";
-    insertMilestone({ id: "M001", title: "New milestone M001", status: "active" });
-    insertArtifact({
-      path: stalePath,
-      artifact_type: "ROADMAP",
-      milestone_id: "M001",
-      slice_id: null,
-      task_id: null,
-      full_content: "# Placeholder roadmap\n",
-    });
-
-    upsertMilestonePlanning("M001", {
-      title: "Lokably brand foundation and welcome page rebuild",
-    });
-
-    assert.equal(getArtifact(stalePath), null, "placeholder-derived artifact row should be removed");
-    assert.equal(
-      getArtifact(finalPath)?.full_content,
-      "# Placeholder roadmap\n",
-      "artifact row should move to the final title-derived phase path",
-    );
-
-    closeDatabase();
-  });
-
   test('gsd-db: active_requirements view excludes superseded', () => {
     openDatabase(':memory:');