gsd-pi 2.78.0-dev.aeeb2ca00 → 2.78.1-dev.84a383f51

package/src/resources/extensions/gsd/commands/handlers/core.ts

@@ -64,16 +64,21 @@ export function showHelp(ctx: ExtensionCommandContext, args = ""): void {
     "  /gsd pause          Pause auto-mode (preserves state, /gsd auto to resume)",
     "  /gsd discuss        Start guided milestone/slice discussion",
     "  /gsd new-milestone  Create milestone from headless context (used by gsd headless)",
+    "  /gsd quick          Execute a quick task without full planning overhead",
+    "  /gsd dispatch       Dispatch a specific phase directly  [research|plan|execute|complete|uat|replan]",
+    "  /gsd parallel       Parallel milestone orchestration  [start|status|stop|pause|resume|merge|watch]",
+    "  /gsd workflow       Custom workflow lifecycle  [new|run|list|validate|pause|resume]",
     "",
     "VISIBILITY",
     `  /gsd status         Show progress dashboard  (${formattedShortcutPair("dashboard")})`,
     `  /gsd parallel watch Open parallel worker monitor  (${formattedShortcutPair("parallel")})`,
+    "  /gsd widget         Cycle status widget  [full|small|min|off]",
     "  /gsd visualize      Interactive 10-tab TUI (progress, timeline, deps, metrics, health, agent, changes, knowledge, captures, export)",
     "  /gsd queue          Show queued/dispatched units and execution order",
     "  /gsd history        View execution history  [--cost] [--phase] [--model] [N]",
     "  /gsd changelog      Show categorized release notes  [version]",
     `  /gsd notifications  View persistent notification history  [clear|tail|filter]  (${formattedShortcutPair("notifications")})`,
-    "  /gsd logs           Browse activity logs, debug logs, and metrics",
+    "  /gsd logs           Browse activity logs, debug logs, and metrics  [debug|tail|clear]",
     "  /gsd debug          Create/list/continue persistent debug sessions",
     "",
     "COURSE CORRECTION",
@@ -82,6 +87,9 @@ export function showHelp(ctx: ExtensionCommandContext, args = ""): void {
     "  /gsd triage         Classify and route pending captures",
     "  /gsd skip <unit>    Prevent a unit from auto-mode dispatch",
     "  /gsd undo           Revert last completed unit  [--force]",
+    "  /gsd undo-task      Reset a specific task's completion state  [DB + markdown]",
+    "  /gsd reset-slice    Reset a slice and all its tasks  [DB + markdown]",
+    "  /gsd rate           Rate last unit's model tier  [over|ok|under]",
     "  /gsd rethink        Conversational project reorganization — reorder, park, discard, add milestones",
     "  /gsd park [id]      Park a milestone — skip without deleting  [reason]",
     "  /gsd unpark [id]    Reactivate a parked milestone",
@@ -90,6 +98,15 @@ export function showHelp(ctx: ExtensionCommandContext, args = ""): void {
     "  /gsd knowledge <type> <text>   Add rule, pattern, or lesson to KNOWLEDGE.md",
     "  /gsd codebase [generate|update|stats]   Manage the CODEBASE.md cache used in prompt context",
     "",
+    "SHIPPING & BACKLOG",
+    "  /gsd ship           Create a PR from milestone artifacts  [--dry-run|--draft|--base|--force]",
+    "  /gsd do <text>      Route freeform text to the right GSD command",
+    "  /gsd session-report Show session cost, tokens, and work summary  [--json|--save]",
+    "  /gsd backlog        Manage backlog items  [add|promote|remove|list]",
+    "  /gsd pr-branch      Create a clean PR branch filtering .gsd/ commits  [--dry-run|--name]",
+    "  /gsd add-tests      Generate tests for completed slices",
+    "  /gsd scan           Rapid codebase assessment  [--focus tech|arch|quality|concerns|tech+arch]",
+    "",
     "SETUP & CONFIGURATION",
     "  /gsd onboarding     Re-run setup wizard  [--resume|--reset|--step <name>]",
     "  /gsd setup          Configuration hub  [llm|model|search|remote|keys|prefs|onboarding]",
@@ -102,18 +119,22 @@ export function showHelp(ctx: ExtensionCommandContext, args = ""): void {
     "  /gsd config         (deprecated) Set tool API keys — use /gsd keys instead",
     "  /gsd show-config    Show effective configuration (models, routing, toggles)",
     "  /gsd hooks          Show post-unit hook configuration",
+    "  /gsd run-hook       Manually trigger a specific hook",
+    "  /gsd skill-health   Skill lifecycle dashboard",
     "  /gsd extensions     Manage extensions  [list|enable|disable|info]",
     "  /gsd fast           Toggle OpenAI service tier  [on|off|flex|status]",
     "  /gsd mcp            MCP server status and connectivity  [status|check <server>|init [dir]]",
     "",
     "MAINTENANCE",
     "  /gsd doctor         Diagnose and repair .gsd/ state  [audit|fix|heal] [scope]",
+    "  /gsd forensics      Examine execution logs and post-mortem analysis",
     "  /gsd export         Export milestone/slice results  [--json|--markdown|--html] [--all]",
     "  /gsd cleanup        Remove merged branches or snapshots  [branches|snapshots]",
     "  /gsd migrate        Migrate .planning/ (v1) to .gsd/ (v2) format",
     "  /gsd remote         Control remote auto-mode  [slack|discord|status|disconnect]",
     "  /gsd inspect        Show SQLite DB diagnostics (schema, row counts, recent entries)",
     "  /gsd update         Update GSD to the latest version via npm",
+    "  /gsd language       Set or clear the global response language  [off|clear|<language>]",
   ];
   const full = ["full", "--full", "all"].includes(args.trim().toLowerCase());
   ctx.ui.notify((full ? fullLines : summaryLines).join("\n"), "info");

package/src/resources/extensions/gsd/commands-mcp-status.ts

@@ -13,6 +13,7 @@
 import type { ExtensionCommandContext } from "@gsd/pi-coding-agent";
 
 import { existsSync, readFileSync } from "node:fs";
+import { homedir } from "node:os";
 import { join, resolve } from "node:path";
 
 import { ensureProjectWorkflowMcpConfig } from "./mcp-project-config.js";
@@ -69,6 +70,7 @@ function readMcpConfigs(): McpServerRawConfig[] {
   const configPaths = [
     join(process.cwd(), ".mcp.json"),
     join(process.cwd(), ".gsd", "mcp.json"),
+    join(process.env.GSD_HOME || join(homedir(), ".gsd"), "mcp.json"),
   ];
 
   for (const configPath of configPaths) {
@@ -118,7 +120,7 @@ export function formatMcpStatusReport(servers: McpServerStatus[]): string {
     return [
       "No MCP servers configured.",
       "",
-      "Add servers to .mcp.json or .gsd/mcp.json to enable MCP integrations.",
+      "Add servers to .mcp.json, .gsd/mcp.json, or $GSD_HOME/mcp.json (default: ~/.gsd/mcp.json) to enable MCP integrations.",
       "Tip: run /gsd mcp init . to write the local GSD workflow MCP config.",
       "See: https://modelcontextprotocol.io/quickstart",
     ].join("\n");

package/src/resources/extensions/gsd/commands-prefs-wizard.ts

@@ -1524,6 +1524,18 @@ async function configureAdvanced(ctx: ExtensionCommandContext, prefs: Record<str
   const tokenCost = await promptBoolean(ctx, "Show token cost in footer", prefs.show_token_cost, false);
   if (tokenCost !== undefined) prefs.show_token_cost = tokenCost;
 
+  const minRequestInterval = await promptInteger(
+    ctx,
+    "Minimum interval between auto-mode LLM requests (ms, 0 to disable)",
+    prefs.min_request_interval_ms,
+    "0",
+  );
+  if (minRequestInterval === "clear") {
+    delete prefs.min_request_interval_ms;
+  } else if (minRequestInterval !== undefined) {
+    prefs.min_request_interval_ms = minRequestInterval;
+  }
+
   const widget = await promptEnum(ctx, "Auto-mode widget display", prefs.widget_mode, ["full", "small", "min", "off"], "full");
   if (widget !== undefined) prefs.widget_mode = widget;
 
@@ -1715,8 +1727,10 @@ export function serializePreferencesToFrontmatter(prefs: Record<string, unknown>
     "budget_ceiling", "budget_enforcement", "context_pause_threshold",
     "notifications", "cmux", "remote_questions", "git",
     "stale_commit_threshold_minutes",
+    "min_request_interval_ms",
     "post_unit_hooks", "pre_dispatch_hooks",
-    "dynamic_routing", "uok", "token_profile", "service_tier", "flat_rate_providers",
+    "dynamic_routing", "disabled_model_providers", "uok", "token_profile",
+    "service_tier", "flat_rate_providers",
     "phases", "parallel", "slice_parallel",
     "reactive_execution", "gate_evaluation",
     "auto_visualize", "auto_report",

package/src/resources/extensions/gsd/dashboard-overlay.ts

@@ -21,7 +21,7 @@ import {
   type UnitMetrics,
 } from "./metrics.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
-import { getActiveWorktreeName } from "./worktree-command.js";
+import { getActiveWorktreeName } from "./worktree-session-state.js";
 import { getWorkerBatches, hasActiveWorkers, type WorkerEntry } from "../subagent/worker-registry.js";
 import { formatDuration, padRight, joinColumns, centerLine, fitColumns, STATUS_GLYPH, STATUS_COLOR } from "../shared/mod.js";
 import { estimateTimeRemaining } from "./auto-dashboard.js";

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

@@ -126,6 +126,8 @@ Setting `prefer_skills: []` does **not** disable skill discovery — it just mea
   - `idle_timeout_minutes`: minutes of inactivity before the supervisor intervenes (default: 10).
   - `hard_timeout_minutes`: minutes before the supervisor forces termination (default: 30).
 
+- `min_request_interval_ms`: number — minimum integer milliseconds between auto-mode LLM request dispatches. Non-integer values are rounded down (e.g., `1000.9 → 1000`). Use this to proactively slow auto-mode on rate-limited providers and reduce 429 errors. Set to `0` to disable. Default: `0` (disabled).
+
 - `git`: configures GSD's git behavior. All fields are optional — omit any to use defaults. Keys:
   - `auto_push`: boolean — automatically push commits to the remote after committing. Default: `false`.
   - `push_branches`: boolean — push the milestone branch to the remote after commits. Default: `false`.
@@ -193,6 +195,8 @@ Setting `prefer_skills: []` does **not** disable skill discovery — it just mea
   - `hooks`: boolean — enable routing hooks. Default: `true`.
   - `capability_routing`: boolean — enable capability-profile scoring for model selection within a tier. Requires `enabled: true`. Default: `false`.
 
+- `disabled_model_providers`: string[] — provider IDs to hide from model selection and routing (for example `["google-gemini-cli"]`). This only affects model availability (`/model`, auto-model selection, routing); it does not disable tool auth flows like `google_search`.
+
 - `uok`: Unified Orchestration Kernel controls. Keys:
   - `enabled`: boolean — enable kernel wrappers and contract observers. Default: `true`.
   - `legacy_fallback.enabled`: boolean — emergency release fallback that forces legacy orchestration behavior even when `uok.enabled` is `true`. Default: `false`.

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

@@ -4,7 +4,7 @@ import { basename, dirname, join } from "node:path";
 import type { DoctorIssue, DoctorIssueCode } from "./doctor-types.js";
 import { cleanNumberedGsdVariants } from "./repo-identity.js";
 import { milestonesDir, gsdRoot, resolveGsdRootFile } from "./paths.js";
-import { deriveState } from "./state.js";
+import { deriveState, isGhostMilestone, isReusableGhostMilestone } from "./state.js";
 import { saveFile } from "./files.js";
 import { nativeIsRepo, nativeForEachRef, nativeUpdateRef } from "./native-git-bridge.js";
 import { readCrashLock, isLockProcessAlive, clearLock } from "./crash-recovery.js";
@@ -12,6 +12,7 @@ import { ensureGitignore, isGsdGitignored } from "./gitignore.js";
 import { readAllSessionStatuses, isSessionStale, removeSessionStatus } from "./session-status-io.js";
 import { recoverFailedMigration } from "./migrate-external.js";
 import { splitCompletedKey } from "./forensics.js";
+import { findMilestoneIds } from "./milestone-ids.js";
 
 export async function checkRuntimeHealth(
   basePath: string,
@@ -593,6 +594,43 @@ export async function checkRuntimeHealth(
   } catch {
     // Non-fatal — snapshot ref check failed
   }
+
+  // ── Orphan milestone directories (#4996) ──────────────────────────────
+  // Walk every milestone ID on disk. Any dir that has no DB row, no worktree,
+  // and no content files is an orphaned stub — it skews nextMilestoneId and
+  // was likely created by ensurePreconditions or showHeadlessMilestoneCreation
+  // for a phantom forward-reference. Surface as a fixable warning.
+  try {
+    const milestoneIds = findMilestoneIds(basePath);
+    const hasDbFile = existsSync(join(root, "gsd.db"));
+    for (const mid of milestoneIds) {
+      const isOrphan = isReusableGhostMilestone(basePath, mid)
+        || (!hasDbFile && isGhostMilestone(basePath, mid));
+      if (isOrphan) {
+        issues.push({
+          severity: "warning",
+          code: "orphan_milestone_dir",
+          scope: "milestone",
+          unitId: mid,
+          message: `Orphan milestone directory: ${mid} — directory exists on disk with no DB row, no worktree, and no content files. This stub skews milestone ID generation and should be removed.`,
+          file: `.gsd/milestones/${mid}`,
+          fixable: true,
+        });
+
+        if (shouldFix("orphan_milestone_dir")) {
+          try {
+            const orphanPath = join(milestonesDir(basePath), mid);
+            rmSync(orphanPath, { recursive: true, force: true });
+            fixesApplied.push(`removed orphan milestone directory: ${mid}`);
+          } catch {
+            // Non-fatal — leave for manual cleanup
+          }
+        }
+      }
+    }
+  } catch {
+    // Non-fatal — orphan milestone directory check failed
+  }
 }
 
 /**

package/src/resources/extensions/gsd/doctor-types.ts

@@ -80,7 +80,9 @@ export type DoctorIssueCode =
   | "db_done_task_no_summary"
   | "db_duplicate_id"
   | "db_unavailable"
-  | "projection_drift";
+  | "projection_drift"
+  // Milestone filesystem/DB drift (#4996)
+  | "orphan_milestone_dir";
 
 /**
  * Issue codes that represent global or completion-critical state.

package/src/resources/extensions/gsd/error-classifier.ts

@@ -59,7 +59,7 @@ const NETWORK_RE = /network|ECONNRESET|ETIMEDOUT|ECONNREFUSED|socket hang up|fet
 // Context overflow errors (context window/length exceeded) should be treated as server-class
 // transient errors so auto-mode can retry with reduced budget or fall back to a larger-context model.
 // See: https://github.com/gsd-build/gsd-2/issues/4528
-const SERVER_RE = /internal server error|500|502|503|overloaded|server_error|api_error|service.?unavailable|context (?:window|length) exceed|context window exceed/i;
+const SERVER_RE = /internal(?: server)?[ _-]?error|500|502|503|overloaded|server_error|api_error|service.?unavailable|context (?:window|length) exceed|context window exceed/i;
 // ECONNRESET/ECONNREFUSED are in NETWORK_RE (same-model retry first).
 const CONNECTION_RE = /terminated|connection.?(?:refused|error)|other side closed|EPIPE|network.?(?:is\s+)?unavailable|stream_exhausted(?:_without_result)?/i;
 // Catch-all for V8 JSON.parse errors: all modern variants end with "in JSON at position \d+".

package/src/resources/extensions/gsd/forensics.ts

@@ -804,7 +804,7 @@ function detectMissingArtifacts(completedKeys: string[], basePath: string, activ
  * the forensics memory-bloat guard in forensics-journal.test.ts — per-event
  * detail stays in the journal itself where the LLM can query it on demand.
  */
-function detectWorktreeOrphans(
+export function detectWorktreeOrphans(
   summary: WorktreeTelemetrySummary,
   anomalies: ForensicAnomaly[],
 ): void {
@@ -822,7 +822,7 @@ function detectWorktreeOrphans(
         reason === "in-progress-unmerged"
           ? "Auto-mode exited without completing a milestone; live work sits on an unmerged milestone branch. Run `/gsd auto` to resume, or merge manually."
           : reason === "complete-unmerged"
-            ? "A completed milestone's branch was never merged back to main. Run `/gsd health --fix` to resolve."
+            ? "A completed milestone's branch was never merged back to main. Run `/gsd doctor fix` to resolve."
             : `Reason: ${reason}.`,
     });
   }

package/src/resources/extensions/gsd/git-service.ts

@@ -38,6 +38,7 @@ import {
 } from "./native-git-bridge.js";
 import { GSDError, GSD_MERGE_CONFLICT, GSD_GIT_ERROR } from "./errors.js";
 import { getErrorMessage } from "./error-utils.js";
+import { isInfrastructureError } from "./auto/infra-errors.js";
 
 // ─── Types ─────────────────────────────────────────────────────────────────
 
@@ -991,6 +992,17 @@ function buildTurnSnapshotLabel(unitType: string, unitId: string): string {
     .replace(/^[-/]+|[-/]+$/g, "") || "turn";
 }
 
+export function handleTurnGitActionError(action: TurnGitActionMode, err: unknown): TurnGitActionResult {
+  if (isInfrastructureError(err)) {
+    throw err;
+  }
+  return {
+    action,
+    status: "failed",
+    error: getErrorMessage(err),
+  };
+}
+
 export function runTurnGitAction(args: {
   basePath: string;
   action: TurnGitActionMode;
@@ -1029,11 +1041,7 @@ export function runTurnGitAction(args: {
       dirty: nativeHasChanges(args.basePath),
     };
   } catch (err) {
-    return {
-      action: args.action,
-      status: "failed",
-      error: getErrorMessage(err),
-    };
+    return handleTurnGitActionError(args.action, err);
   }
 }
 

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

@@ -1405,6 +1405,16 @@ export function checkpointDatabase(): void {
 
 let _txDepth = 0;
 
+/**
+ * Whether the current call is running inside an active SQLite transaction.
+ * Statement-time recovery paths (e.g. VACUUM retry on a malformed memory
+ * store) MUST gate on this — SQLite refuses VACUUM inside a transaction
+ * and would mask the original error with a secondary "cannot VACUUM" throw.
+ */
+export function isInTransaction(): boolean {
+  return _txDepth > 0;
+}
+
 export function transaction<T>(fn: () => T): T {
   if (!currentDb) throw new GSDError(GSD_STALE_STATE, "gsd-db: No database open");
 
@@ -1419,8 +1429,8 @@ export function transaction<T>(fn: () => T): T {
     }
   }
 
-  _txDepth++;
   currentDb.exec("BEGIN");
+  _txDepth++;
   try {
     const result = fn();
     currentDb.exec("COMMIT");
@@ -1452,8 +1462,8 @@ export function readTransaction<T>(fn: () => T): T {
     }
   }
 
-  _txDepth++;
   currentDb.exec("BEGIN DEFERRED");
+  _txDepth++;
   try {
     const result = fn();
     currentDb.exec("COMMIT");

package/src/resources/extensions/gsd/guided-flow.ts

@@ -44,7 +44,9 @@ import { showProjectInit, offerMigration } from "./init-wizard.js";
 import { validateDirectory } from "./validate-directory.js";
 import { showConfirm } from "../shared/tui.js";
 import { debugLog } from "./debug-logger.js";
-import { findMilestoneIds, nextMilestoneId, reserveMilestoneId, getReservedMilestoneIds, clearReservedMilestoneIds } from "./milestone-ids.js";
+import { findMilestoneIds, clearReservedMilestoneIds } from "./milestone-ids.js";
+import { nextMilestoneIdReserved } from "./milestone-id-reservation.js";
+export { nextMilestoneIdReserved } from "./milestone-id-reservation.js";
 import { parkMilestone, discardMilestone } from "./milestone-actions.js";
 import { selectAndApplyModel } from "./auto-model-selection.js";
 import { DISCUSS_TOOLS_ALLOWLIST } from "./constants.js";
@@ -72,20 +74,6 @@ export {
 } from "./guided-flow-queue.js";
 import { logWarning } from "./workflow-logger.js";
 
-// ─── ID Generation with Reservation ─────────────────────────────────────────
-
-/**
- * Generate the next milestone ID, accounting for reserved IDs, and reserve it.
- * Ensures any preview ID shown in the UI matches what `gsd_milestone_generate_id`
- * will later return.
- */
-function nextMilestoneIdReserved(existingIds: string[], uniqueEnabled: boolean): string {
-  const allIds = [...new Set([...existingIds, ...getReservedMilestoneIds()])];
-  const id = nextMilestoneId(allIds, uniqueEnabled);
-  reserveMilestoneId(id);
-  return id;
-}
-
 function needsPlanV2Gate(state: GSDState): boolean {
   return state.phase === "executing"
     || state.phase === "summarizing"
@@ -832,14 +820,19 @@ export async function showHeadlessMilestoneCreation(
   // Ensure .gsd/ is bootstrapped
   bootstrapGsdProject(basePath);
 
+  const { ensureDbOpen } = await import("./bootstrap/dynamic-tools.js");
+  await ensureDbOpen(basePath);
+
   // Generate next milestone ID
   const existingIds = findMilestoneIds(basePath);
   const prefs = loadEffectiveGSDPreferences();
-  const nextId = nextMilestoneIdReserved(existingIds, prefs?.preferences?.unique_milestone_ids ?? false);
+  const nextId = nextMilestoneIdReserved(existingIds, prefs?.preferences?.unique_milestone_ids ?? false, basePath);
 
-  // Create milestone directory
-  const milestoneDir = join(gsdRoot(basePath), "milestones", nextId, "slices");
-  mkdirSync(milestoneDir, { recursive: true });
+  // Fix #4996: Do NOT pre-create the milestone directory here.
+  // atomicWriteAsync (used by all artifact writers) calls mkdir lazily before
+  // each write, so every path through saveArtifactToDb / saveFile is already
+  // lazy-mkdir-safe. Pre-creating the dir before the discuss flow runs leaves
+  // an orphan stub if discuss is abandoned — that stub later skews nextMilestoneId.
 
   // Build and dispatch the headless discuss prompt
   const prompt = buildHeadlessDiscussPrompt(nextId, seedContext, basePath);
@@ -1054,9 +1047,11 @@ export async function showDiscuss(
         fastPathInstruction: "",
       }), "gsd-discuss", ctx, "discuss-milestone");
     } else if (choice === "skip_milestone") {
+      const { ensureDbOpen } = await import("./bootstrap/dynamic-tools.js");
+      await ensureDbOpen(basePath);
       const milestoneIds = findMilestoneIds(basePath);
       const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-      const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+      const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
       pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: false, createdAt: Date.now() });
       await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId, `New milestone ${nextId}.`, basePath), "gsd-run", ctx, "discuss-milestone");
     }
@@ -1461,7 +1456,7 @@ async function handleMilestoneActions(
   if (choice === "skip") {
     const milestoneIds = findMilestoneIds(basePath);
     const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-    const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+    const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
     pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
     await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId,
       `New milestone ${nextId}.`,
@@ -1546,6 +1541,11 @@ export async function showSmartEntry(
   ensureGitignore(basePath);
   untrackRuntimeFiles(basePath);
 
+  {
+    const { ensureDbOpen } = await import("./bootstrap/dynamic-tools.js");
+    await ensureDbOpen(basePath);
+  }
+
   // ── Self-heal stale runtime records from crashed auto-mode sessions ──
   selfHealRuntimeRecords(basePath, ctx);
 
@@ -1648,7 +1648,7 @@ export async function showSmartEntry(
     }
 
     const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-    const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+    const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
     const isFirst = milestoneIds.length === 0;
 
     if (isFirst) {
@@ -1728,7 +1728,7 @@ export async function showSmartEntry(
     if (choice === "new_milestone") {
       const milestoneIds = findMilestoneIds(basePath);
       const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-      const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+      const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
 
       pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
       await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId,
@@ -1796,7 +1796,7 @@ export async function showSmartEntry(
     } else if (choice === "skip_milestone") {
       const milestoneIds = findMilestoneIds(basePath);
       const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-      const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+      const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
       pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
       await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId,
         `New milestone ${nextId}.`,
@@ -1893,7 +1893,7 @@ export async function showSmartEntry(
       } else if (choice === "skip_milestone") {
         const milestoneIds = findMilestoneIds(basePath);
         const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-        const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+        const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
         pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
         await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId,
           `New milestone ${nextId}.`,

package/src/resources/extensions/gsd/memory-store.ts

@@ -7,6 +7,7 @@ import {
   isDbAvailable,
   _getAdapter,
   transaction,
+  isInTransaction,
   insertMemoryRow,
   rewriteMemoryId,
   updateMemoryContentRow,
@@ -19,6 +20,7 @@ import {
   deleteMemoryRelationsFor,
 } from './gsd-db.js';
 import { createMemoryRelation, isValidRelation } from './memory-relations.js';
+import { logWarning } from './workflow-logger.js';
 
 // ─── Types ──────────────────────────────────────────────────────────────────
 
@@ -487,7 +489,13 @@ export function nextMemoryId(): string {
  * Insert a new memory with a race-safe auto-assigned ID.
  * Uses AUTOINCREMENT seq to derive the ID after insert, avoiding
  * the read-then-write race in concurrent scenarios (e.g. worktrees).
- * Returns the assigned ID, or null on failure.
+ * Returns the assigned ID, or null when the DB is unavailable.
+ *
+ * Throws on genuine SQL errors (corruption, missing tables, constraint
+ * violations) so callers can surface the underlying message instead of
+ * collapsing the failure to a generic "create_failed". See issue #4967 —
+ * the previous bare-catch swallowed "database disk image is malformed"
+ * errors, leaving the memory subsystem broken without any signal.
  */
 export function createMemory(fields: {
   category: string;
@@ -504,34 +512,70 @@ export function createMemory(fields: {
   if (!adapter) return null;
 
   try {
-    const now = new Date().toISOString();
-    // Insert with a temporary placeholder ID — seq is auto-assigned
-    const placeholder = `_TMP_${Date.now()}_${Math.random().toString(36).slice(2, 8)}`;
-    insertMemoryRow({
-      id: placeholder,
-      category: fields.category,
-      content: fields.content,
-      confidence: fields.confidence ?? 0.8,
-      sourceUnitType: fields.source_unit_type ?? null,
-      sourceUnitId: fields.source_unit_id ?? null,
-      createdAt: now,
-      updatedAt: now,
-      scope: fields.scope ?? 'project',
-      tags: fields.tags ?? [],
-      structuredFields: fields.structuredFields ?? null,
-    });
-    // Derive the real ID from the assigned seq (SELECT is still fine via adapter)
-    const row = adapter.prepare('SELECT seq FROM memories WHERE id = :id').get({ ':id': placeholder });
-    if (!row) return placeholder; // fallback — should not happen
-    const seq = row['seq'] as number;
-    const realId = `MEM${String(seq).padStart(3, '0')}`;
-    rewriteMemoryId(placeholder, realId);
-    return realId;
-  } catch {
-    return null;
+    return transaction(() => doCreateMemory(adapter, fields));
+  } catch (err) {
+    const message = err instanceof Error ? err.message : String(err);
+
+    // Targeted recovery: a malformed memory store can sometimes be rebuilt
+    // by VACUUM. Skip when inside a transaction — SQLite refuses VACUUM
+    // there and a secondary throw would mask the real fault.
+    if (message.toLowerCase().includes('malformed') && !isInTransaction()) {
+      try {
+        adapter.prepare('VACUUM').run();
+        const recoveryMessage = 'recovered malformed memory store via VACUUM';
+        process.stderr.write(`memory-store: ${recoveryMessage}\n`);
+        logWarning('memory-store', recoveryMessage);
+        return transaction(() => doCreateMemory(adapter, fields));
+      } catch (retryErr) {
+        const retryMsg = retryErr instanceof Error ? retryErr.message : String(retryErr);
+        logWarning('memory-store', `VACUUM recovery for memory store failed: ${retryMsg}`);
+        // Surface the *original* malformed error — it's the actionable signal.
+        throw err;
+      }
+    }
+
+    throw err;
   }
 }
 
+function doCreateMemory(
+  adapter: NonNullable<ReturnType<typeof _getAdapter>>,
+  fields: {
+    category: string;
+    content: string;
+    confidence?: number;
+    source_unit_type?: string;
+    source_unit_id?: string;
+    scope?: string;
+    tags?: string[];
+    structuredFields?: Record<string, unknown> | null;
+  },
+): string {
+  const now = new Date().toISOString();
+  // Insert with a temporary placeholder ID — seq is auto-assigned
+  const placeholder = `_TMP_${Date.now()}_${Math.random().toString(36).slice(2, 8)}`;
+  insertMemoryRow({
+    id: placeholder,
+    category: fields.category,
+    content: fields.content,
+    confidence: fields.confidence ?? 0.8,
+    sourceUnitType: fields.source_unit_type ?? null,
+    sourceUnitId: fields.source_unit_id ?? null,
+    createdAt: now,
+    updatedAt: now,
+    scope: fields.scope ?? 'project',
+    tags: fields.tags ?? [],
+    structuredFields: fields.structuredFields ?? null,
+  });
+  // Derive the real ID from the assigned seq (SELECT is still fine via adapter)
+  const row = adapter.prepare('SELECT seq FROM memories WHERE id = :id').get({ ':id': placeholder });
+  if (!row) return placeholder; // fallback — should not happen
+  const seq = row['seq'] as number;
+  const realId = `MEM${String(seq).padStart(3, '0')}`;
+  rewriteMemoryId(placeholder, realId);
+  return realId;
+}
+
 /**
  * Update a memory's content and optionally its confidence.
  */
@@ -728,8 +772,17 @@ export function applyMemoryActions(
       }
       enforceMemoryCap();
     });
-  } catch {
-    // non-fatal — transaction will have rolled back
+  } catch (err) {
+    // Non-fatal — the transaction has rolled back. We log a warning so a
+    // degraded memory subsystem (e.g. malformed store, missing tables) is
+    // visible to forensics instead of silently dropping every CREATE — see
+    // issue #4967, where this swallow combined with createMemory's bare
+    // catch hid SQLite corruption from the auto-mode flow entirely.
+    const message = err instanceof Error ? err.message : String(err);
+    logWarning(
+      'memory-store',
+      `applyMemoryActions failed (memory subsystem degraded): ${message}`,
+    );
   }
 }