gsd-pi 2.65.0-dev.5c8557b → 2.65.0-dev.800ece0

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

@@ -8,6 +8,7 @@ import { runEnvironmentChecks } from "../../doctor-environment.js";
 import { deriveState } from "../../state.js";
 import { handleCmux } from "../../commands-cmux.js";
 import { projectRoot } from "../context.js";
+import { formatShortcut } from "../../files.js";
 
 export function showHelp(ctx: ExtensionCommandContext): void {
   const lines = [
@@ -24,12 +25,12 @@ export function showHelp(ctx: ExtensionCommandContext): void {
     "  /gsd new-milestone  Create milestone from headless context (used by gsd headless)",
     "",
     "VISIBILITY",
-    "  /gsd status         Show progress dashboard  (Ctrl+Alt+G)",
+    `  /gsd status         Show progress dashboard  (${formatShortcut("Ctrl+Alt+G")})`,
     "  /gsd visualize      Interactive 10-tab TUI (progress, timeline, deps, metrics, health, agent, changes, knowledge, captures, export)",
     "  /gsd queue          Show queued/dispatched units and execution order",
     "  /gsd history        View execution history  [--cost] [--phase] [--model] [N]",
     "  /gsd changelog      Show categorized release notes  [version]",
-    "  /gsd notifications  View persistent notification history  [clear|tail|filter]  (Ctrl+Alt+N)",
+    `  /gsd notifications  View persistent notification history  [clear|tail|filter]  (${formatShortcut("Ctrl+Alt+N")})`,
     "",
     "COURSE CORRECTION",
     "  /gsd steer <desc>   Apply user override to active work",
@@ -52,6 +53,7 @@ export function showHelp(ctx: ExtensionCommandContext): void {
     "  /gsd cmux           Manage cmux integration  [status|on|off|notifications|sidebar|splits|browser]",
     "  /gsd config         Set API keys for external tools",
     "  /gsd keys           API key manager  [list|add|remove|test|rotate|doctor]",
+    "  /gsd show-config    Show effective configuration (models, routing, toggles)",
     "  /gsd hooks          Show post-unit hook configuration",
     "  /gsd extensions     Manage extensions  [list|enable|disable|info]",
     "  /gsd fast           Toggle OpenAI service tier  [on|off|flex|status]",
@@ -71,6 +73,9 @@ export function showHelp(ctx: ExtensionCommandContext): void {
 
 export async function handleStatus(ctx: ExtensionCommandContext): Promise<void> {
   const basePath = projectRoot();
+  // Open DB in cold sessions so status uses DB-backed state, not filesystem fallback (#3385)
+  const { ensureDbOpen } = await import("../../bootstrap/dynamic-tools.js");
+  await ensureDbOpen();
   const state = await deriveState(basePath);
 
   if (state.registry.length === 0) {
@@ -214,6 +219,25 @@ export async function handleCoreCommand(trimmed: string, ctx: ExtensionCommandCo
     await handleCmux(trimmed.replace(/^cmux\s*/, "").trim(), ctx);
     return true;
   }
+  if (trimmed === "show-config") {
+    const { GSDConfigOverlay, formatConfigText } = await import("../../config-overlay.js");
+    const result = await ctx.ui.custom<void>(
+      (tui, theme, _kb, done) => new GSDConfigOverlay(tui, theme, () => done()),
+      {
+        overlay: true,
+        overlayOptions: {
+          width: "65%",
+          minWidth: 55,
+          maxHeight: "85%",
+          anchor: "center",
+        },
+      },
+    );
+    if (result === undefined) {
+      ctx.ui.notify(formatConfigText(), "info");
+    }
+    return true;
+  }
   if (trimmed === "setup" || trimmed.startsWith("setup ")) {
     await handleSetup(trimmed.replace(/^setup\s*/, "").trim(), ctx);
     return true;

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

@@ -105,7 +105,7 @@ function discoverManifests(): Map<string, ExtensionManifest> {
   const manifests = new Map<string, ExtensionManifest>();
   if (!existsSync(extDir)) return manifests;
   for (const entry of readdirSync(extDir, { withFileTypes: true })) {
-    if (!entry.isDirectory()) continue;
+    if (!entry.isDirectory() && !entry.isSymbolicLink()) continue;
     const m = readManifest(join(extDir, entry.name));
     if (m) manifests.set(m.id, m);
   }

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

@@ -0,0 +1,331 @@
+/**
+ * GSD Configuration Overlay
+ *
+ * Read-only TUI overlay showing the effective GSD configuration:
+ * token profile, model assignments, dynamic routing, git settings,
+ * budget, workflow toggles, and preference file sources.
+ * Opened via `/gsd show-config` or `/gsd config`.
+ */
+
+import type { Theme } from "@gsd/pi-coding-agent";
+import { matchesKey, Key, truncateToWidth } from "@gsd/pi-tui";
+
+import {
+  loadEffectiveGSDPreferences,
+  loadGlobalGSDPreferences,
+  loadProjectGSDPreferences,
+  getGlobalGSDPreferencesPath,
+  getProjectGSDPreferencesPath,
+  resolveDynamicRoutingConfig,
+  resolveEffectiveProfile,
+  resolveModelWithFallbacksForUnit,
+  resolveAutoSupervisorConfig,
+} from "./preferences.js";
+
+// ─── Data Collection ──────────────────────────────────────────────────────
+
+interface ConfigSection {
+  title: string;
+  rows: Array<{ label: string; value: string; accent?: boolean }>;
+}
+
+function collectConfigSections(): ConfigSection[] {
+  const sections: ConfigSection[] = [];
+
+  const globalPrefs = loadGlobalGSDPreferences();
+  const projectPrefs = loadProjectGSDPreferences();
+  const effective = loadEffectiveGSDPreferences();
+  const prefs = effective?.preferences;
+
+  // ─── Sources ─────────────────────────────────────────────────────────
+  sections.push({
+    title: "Sources",
+    rows: [
+      { label: "Global", value: globalPrefs ? globalPrefs.path : `(none) ${getGlobalGSDPreferencesPath()}` },
+      { label: "Project", value: projectPrefs ? projectPrefs.path : `(none) ${getProjectGSDPreferencesPath()}` },
+    ],
+  });
+
+  // ─── Profile ─────────────────────────────────────────────────────────
+  const profile = resolveEffectiveProfile();
+  const profileRows: ConfigSection["rows"] = [
+    { label: "Token profile", value: `${profile}${!prefs?.token_profile ? " (default)" : ""}`, accent: true },
+  ];
+  if (prefs?.mode) profileRows.push({ label: "Workflow mode", value: prefs.mode });
+  sections.push({ title: "Profile", rows: profileRows });
+
+  // ─── Models ──────────────────────────────────────────────────────────
+  const unitTypes: Array<[string, string]> = [
+    ["research", "research-milestone"],
+    ["planning", "plan-milestone"],
+    ["discuss", "discuss-milestone"],
+    ["execution", "execute-task"],
+    ["completion", "complete-slice"],
+    ["validation", "run-uat"],
+  ];
+
+  const modelRows: ConfigSection["rows"] = [];
+  for (const [label, unitType] of unitTypes) {
+    const resolved = resolveModelWithFallbacksForUnit(unitType);
+    if (resolved) {
+      let val = resolved.primary;
+      if (resolved.fallbacks.length > 0) {
+        val += ` \u2192 ${resolved.fallbacks.join(" \u2192 ")}`;
+      }
+      modelRows.push({ label, value: val });
+    } else {
+      modelRows.push({ label, value: "(inherit)" });
+    }
+  }
+
+  // subagent is a direct config key
+  const models = prefs?.models as Record<string, unknown> | undefined;
+  const subVal = models?.subagent;
+  if (subVal) {
+    const model = typeof subVal === "string" ? subVal : (subVal as { model?: string })?.model ?? "?";
+    modelRows.push({ label: "subagent", value: model });
+  } else {
+    modelRows.push({ label: "subagent", value: "(inherit)" });
+  }
+
+  sections.push({ title: "Models", rows: modelRows });
+
+  // ─── Dynamic Routing ─────────────────────────────────────────────────
+  const routing = resolveDynamicRoutingConfig();
+  const routingRows: ConfigSection["rows"] = [
+    { label: "Enabled", value: routing.enabled ? "yes" : "no", accent: routing.enabled },
+  ];
+  if (routing.enabled) {
+    routingRows.push({ label: "Escalate on fail", value: routing.escalate_on_failure !== false ? "yes" : "no" });
+    routingRows.push({ label: "Budget pressure", value: routing.budget_pressure !== false ? "yes" : "no" });
+    routingRows.push({ label: "Cross-provider", value: routing.cross_provider !== false ? "yes" : "no" });
+    if (routing.tier_models) {
+      const tm = routing.tier_models;
+      if (tm.light) routingRows.push({ label: "[L] light", value: tm.light });
+      if (tm.standard) routingRows.push({ label: "[S] standard", value: tm.standard });
+      if (tm.heavy) routingRows.push({ label: "[H] heavy", value: tm.heavy });
+    }
+  }
+  sections.push({ title: "Dynamic Routing", rows: routingRows });
+
+  // ─── Git ─────────────────────────────────────────────────────────────
+  if (prefs?.git) {
+    const g = prefs.git;
+    const gitRows: ConfigSection["rows"] = [];
+    if (g.isolation !== undefined) gitRows.push({ label: "Isolation", value: String(g.isolation) });
+    if (g.auto_push !== undefined) gitRows.push({ label: "Auto push", value: String(g.auto_push) });
+    if (g.push_branches !== undefined) gitRows.push({ label: "Push branches", value: String(g.push_branches) });
+    if (g.merge_strategy) gitRows.push({ label: "Merge strategy", value: g.merge_strategy });
+    if (g.main_branch) gitRows.push({ label: "Main branch", value: g.main_branch });
+    if (g.remote) gitRows.push({ label: "Remote", value: g.remote });
+    if (gitRows.length > 0) sections.push({ title: "Git", rows: gitRows });
+  }
+
+  // ─── Budget ──────────────────────────────────────────────────────────
+  if (prefs?.budget_ceiling !== undefined || prefs?.budget_enforcement) {
+    const budgetRows: ConfigSection["rows"] = [];
+    if (prefs.budget_ceiling !== undefined) budgetRows.push({ label: "Ceiling", value: `$${prefs.budget_ceiling}` });
+    if (prefs.budget_enforcement) budgetRows.push({ label: "Enforcement", value: String(prefs.budget_enforcement) });
+    sections.push({ title: "Budget", rows: budgetRows });
+  }
+
+  // ─── Auto Supervisor ─────────────────────────────────────────────────
+  if (prefs?.auto_supervisor) {
+    const sup = resolveAutoSupervisorConfig();
+    const supRows: ConfigSection["rows"] = [];
+    if (sup.model) supRows.push({ label: "Model", value: sup.model });
+    supRows.push({ label: "Soft timeout", value: `${sup.soft_timeout_minutes}m` });
+    supRows.push({ label: "Idle timeout", value: `${sup.idle_timeout_minutes}m` });
+    supRows.push({ label: "Hard timeout", value: `${sup.hard_timeout_minutes}m` });
+    sections.push({ title: "Auto Supervisor", rows: supRows });
+  }
+
+  // ─── Toggles ─────────────────────────────────────────────────────────
+  const toggleRows: ConfigSection["rows"] = [];
+  if (prefs?.phases) {
+    const p = prefs.phases;
+    if (p.skip_research) toggleRows.push({ label: "skip_research", value: "on" });
+    if (p.skip_reassess) toggleRows.push({ label: "skip_reassess", value: "on" });
+    if (p.skip_slice_research) toggleRows.push({ label: "skip_slice_research", value: "on" });
+    if (p.skip_milestone_validation) toggleRows.push({ label: "skip_milestone_validation", value: "on" });
+    if (p.require_slice_discussion) toggleRows.push({ label: "require_slice_discussion", value: "on" });
+  }
+  if (prefs?.uat_dispatch) toggleRows.push({ label: "uat_dispatch", value: "on" });
+  if (prefs?.auto_visualize) toggleRows.push({ label: "auto_visualize", value: "on" });
+  if (prefs?.auto_report === false) toggleRows.push({ label: "auto_report", value: "off" });
+  if (prefs?.show_token_cost) toggleRows.push({ label: "show_token_cost", value: "on" });
+  if (prefs?.forensics_dedup) toggleRows.push({ label: "forensics_dedup", value: "on" });
+  if (prefs?.unique_milestone_ids) toggleRows.push({ label: "unique_milestone_ids", value: "on" });
+  if (prefs?.service_tier) toggleRows.push({ label: "service_tier", value: prefs.service_tier });
+  if (prefs?.search_provider && prefs.search_provider !== "auto") toggleRows.push({ label: "search_provider", value: prefs.search_provider });
+  if (prefs?.context_selection) toggleRows.push({ label: "context_selection", value: prefs.context_selection });
+  if (prefs?.widget_mode && prefs.widget_mode !== "full") toggleRows.push({ label: "widget_mode", value: prefs.widget_mode });
+  if (prefs?.experimental?.rtk) toggleRows.push({ label: "experimental.rtk", value: "on" });
+  if (toggleRows.length > 0) sections.push({ title: "Toggles", rows: toggleRows });
+
+  // ─── Parallel ────────────────────────────────────────────────────────
+  if (prefs?.parallel) {
+    const pc = prefs.parallel;
+    const parallelRows: ConfigSection["rows"] = [];
+    if (pc.max_workers !== undefined) parallelRows.push({ label: "Max workers", value: String(pc.max_workers) });
+    if (pc.merge_strategy) parallelRows.push({ label: "Merge strategy", value: pc.merge_strategy });
+    if (pc.auto_merge) parallelRows.push({ label: "Auto merge", value: pc.auto_merge });
+    if (parallelRows.length > 0) sections.push({ title: "Parallel", rows: parallelRows });
+  }
+
+  // ─── Hooks ───────────────────────────────────────────────────────────
+  const postHooks = prefs?.post_unit_hooks?.filter(h => h.enabled !== false) ?? [];
+  const preHooks = prefs?.pre_dispatch_hooks?.filter(h => h.enabled !== false) ?? [];
+  if (postHooks.length > 0 || preHooks.length > 0) {
+    const hookRows: ConfigSection["rows"] = [];
+    if (preHooks.length > 0) hookRows.push({ label: "Pre-dispatch", value: `${preHooks.length} active` });
+    if (postHooks.length > 0) hookRows.push({ label: "Post-unit", value: `${postHooks.length} active` });
+    sections.push({ title: "Hooks", rows: hookRows });
+  }
+
+  // ─── Warnings ────────────────────────────────────────────────────────
+  const warnings = [
+    ...(globalPrefs?.warnings ?? []),
+    ...(projectPrefs?.warnings ?? []),
+  ];
+  if (warnings.length > 0) {
+    sections.push({
+      title: "Warnings",
+      rows: warnings.map(w => ({ label: "\u26a0", value: w })),
+    });
+  }
+
+  return sections;
+}
+
+// ─── Plain Text Formatter (headless/RPC fallback) ─────────────────────────
+
+export function formatConfigText(): string {
+  const sections = collectConfigSections();
+  const lines: string[] = ["GSD Configuration\n"];
+
+  let maxLabel = 0;
+  for (const section of sections) {
+    for (const row of section.rows) {
+      if (row.label.length > maxLabel) maxLabel = row.label.length;
+    }
+  }
+  const pad = Math.min(maxLabel + 2, 24);
+
+  for (const section of sections) {
+    lines.push("");
+    lines.push(section.title.toUpperCase());
+    for (const row of section.rows) {
+      lines.push(`  ${row.label.padEnd(pad)}${row.value}`);
+    }
+  }
+
+  return lines.join("\n");
+}
+
+// ─── Overlay Class ────────────────────────────────────────────────────────
+
+export class GSDConfigOverlay {
+  private tui: { requestRender: () => void };
+  private theme: Theme;
+  private onClose: () => void;
+  private sections: ConfigSection[];
+  private cachedLines?: string[];
+  private scrollOffset = 0;
+  private disposed = false;
+
+  constructor(
+    tui: { requestRender: () => void },
+    theme: Theme,
+    onClose: () => void,
+  ) {
+    this.tui = tui;
+    this.theme = theme;
+    this.onClose = onClose;
+    this.sections = collectConfigSections();
+  }
+
+  invalidate(): void {
+    this.cachedLines = undefined;
+  }
+
+  dispose(): void {
+    this.disposed = true;
+  }
+
+  handleInput(data: string): void {
+    if (matchesKey(data, Key.escape) || data === "q") {
+      this.dispose();
+      this.onClose();
+      return;
+    }
+    if (matchesKey(data, Key.down) || data === "j") {
+      this.scrollOffset++;
+      this.cachedLines = undefined;
+      this.tui.requestRender();
+      return;
+    }
+    if (matchesKey(data, Key.up) || data === "k") {
+      this.scrollOffset = Math.max(0, this.scrollOffset - 1);
+      this.cachedLines = undefined;
+      this.tui.requestRender();
+      return;
+    }
+    if (matchesKey(data, Key.pageDown)) {
+      this.scrollOffset += 10;
+      this.cachedLines = undefined;
+      this.tui.requestRender();
+      return;
+    }
+    if (matchesKey(data, Key.pageUp)) {
+      this.scrollOffset = Math.max(0, this.scrollOffset - 10);
+      this.cachedLines = undefined;
+      this.tui.requestRender();
+      return;
+    }
+  }
+
+  render(width: number): string[] {
+    if (this.cachedLines) return this.cachedLines;
+
+    const t = this.theme;
+    const w = Math.max(width, 50);
+    const allLines: string[] = [];
+
+    // Header
+    allLines.push(t.bold(t.fg("accent", " GSD Configuration ")));
+    allLines.push(t.fg("muted", "\u2500".repeat(w)));
+
+    // Find max label width for alignment
+    let maxLabel = 0;
+    for (const section of this.sections) {
+      for (const row of section.rows) {
+        if (row.label.length > maxLabel) maxLabel = row.label.length;
+      }
+    }
+    const labelPad = Math.min(maxLabel + 2, 24);
+
+    for (const section of this.sections) {
+      allLines.push("");
+      allLines.push(t.bold(t.fg("accent", `  ${section.title}`)));
+
+      for (const row of section.rows) {
+        const label = t.fg("muted", `    ${row.label.padEnd(labelPad)}`);
+        const value = row.accent ? t.bold(row.value) : row.value;
+        allLines.push(truncateToWidth(`${label}${value}`, w));
+      }
+    }
+
+    allLines.push("");
+    allLines.push(t.fg("muted", `  ${"\u2500".repeat(w - 4)}`));
+    allLines.push(t.fg("muted", "  esc/q close  \u2502  \u2191\u2193/jk scroll  \u2502  /gsd prefs to edit"));
+
+    // Apply scroll
+    const maxScroll = Math.max(0, allLines.length - 20);
+    this.scrollOffset = Math.min(this.scrollOffset, maxScroll);
+    const visible = allLines.slice(this.scrollOffset);
+
+    this.cachedLines = visible;
+    return visible;
+  }
+}

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

@@ -345,8 +345,12 @@ export async function saveRequirementToDb(
       await saveFile(filePath, md);
     } catch (diskErr) {
       logError('manifest', 'disk write failed, rolling back DB row', { fn: 'saveRequirementToDb', error: String((diskErr as Error).message) });
-      const rollbackAdapter = db._getAdapter();
-      rollbackAdapter?.prepare('DELETE FROM requirements WHERE id = :id').run({ ':id': id });
+      try {
+        const rollbackAdapter = db._getAdapter();
+        rollbackAdapter?.prepare('DELETE FROM requirements WHERE id = :id').run({ ':id': id });
+      } catch (rollbackErr) {
+        logError('manifest', 'SPLIT BRAIN: disk write failed AND DB rollback failed — DB has orphaned row', { fn: 'saveRequirementToDb', id, error: String((rollbackErr as Error).message) });
+      }
       throw diskErr;
     }
     invalidateStateCache();
@@ -466,7 +470,11 @@ export async function saveDecisionToDb(
       await saveFile(filePath, md);
     } catch (diskErr) {
       logError('manifest', 'disk write failed, rolling back DB row', { fn: 'saveDecisionToDb', error: String((diskErr as Error).message) });
-      adapter?.prepare('DELETE FROM decisions WHERE id = :id').run({ ':id': id });
+      try {
+        adapter?.prepare('DELETE FROM decisions WHERE id = :id').run({ ':id': id });
+      } catch (rollbackErr) {
+        logError('manifest', 'SPLIT BRAIN: disk write failed AND DB rollback failed — DB has orphaned row', { fn: 'saveDecisionToDb', id, error: String((rollbackErr as Error).message) });
+      }
       throw diskErr;
     }
     // #2661: When a decision defers a slice, update the slice status in the DB

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

@@ -1114,7 +1114,7 @@ function resolveVersionCatalogAccessors(
   return accessors;
 }
 
-function scanProjectFiles(basePath: string): string[] {
+export function scanProjectFiles(basePath: string): string[] {
   const files: string[] = [];
   const queue: Array<{ path: string; depth: number }> = [{ path: basePath, depth: 0 }];
 

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

@@ -5,6 +5,7 @@ import { findMilestoneIds } from "./guided-flow.js";
 import { parseUnitId } from "./unit-id.js";
 import { isDbAvailable, getMilestoneSlices } from "./gsd-db.js";
 import { parseRoadmap } from "./parsers-legacy.js";
+import { isClosedStatus } from "./status-guards.js";
 import { readFileSync } from "node:fs";
 
 const SLICE_DISPATCH_TYPES = new Set([
@@ -57,7 +58,7 @@ export function getPriorSliceCompletionBlocker(
       if (rows.length > 0) {
         slices = rows.map((r) => ({
           id: r.id,
-          done: r.status === "complete",
+          done: isClosedStatus(r.status),
           depends: r.depends ?? [],
         }));
       }

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

@@ -211,6 +211,7 @@ Setting `prefer_skills: []` does **not** disable skill discovery — it just mea
   - `budget_ceiling`: number — optional per-parallel-run budget ceiling.
   - `merge_strategy`: `"per-slice"` or `"per-milestone"` — when to merge worktree results back. Default: `"per-milestone"`.
   - `auto_merge`: `"auto"`, `"confirm"`, or `"manual"` — merge behavior after completion. `"auto"` merges immediately; `"confirm"` asks first; `"manual"` leaves branches for you. Default: `"confirm"`.
+  - `worker_model`: string — optional model override for parallel milestone workers. When set, workers use this model (e.g. `"claude-haiku-4-5"`) instead of inheriting the coordinator's model. Useful for cost savings on execution-heavy milestones.
 
 - `verification_commands`: string[] — shell commands to run as verification after task execution (e.g., `["npm test", "npm run lint"]`). Commands run in order; if any fails, the task is marked as needing fixes.
 

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

@@ -87,7 +87,8 @@ function validatePreferenceShape(preferences: GSDPreferences): string[] {
   return issues;
 }
 
-function buildStateMarkdown(state: Awaited<ReturnType<typeof deriveState>>): string {
+/** Build STATE.md content from derived state. Exported for guided-flow pre-dispatch rebuild (#3475). */
+export function buildStateMarkdown(state: Awaited<ReturnType<typeof deriveState>>): string {
   const lines: string[] = [];
   lines.push("# GSD State", "");
 

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

@@ -70,6 +70,25 @@ export function clearParseCache(): void {
   for (const cb of _cacheClearCallbacks) cb();
 }
 
+// ─── Platform shortcuts ───────────────────────────────────────────────────
+
+const IS_MAC = process.platform === "darwin";
+
+/**
+ * Format a keyboard shortcut for the current OS.
+ * Input: modifier key combo like "Ctrl+Alt+G"
+ * Output: "⌃⌥G" on macOS, "Ctrl+Alt+G" on Windows/Linux.
+ */
+export function formatShortcut(combo: string): string {
+  if (!IS_MAC) return combo;
+  return combo
+    .replace(/Ctrl\+Alt\+/i, "⌃⌥")
+    .replace(/Ctrl\+/i, "⌃")
+    .replace(/Alt\+/i, "⌥")
+    .replace(/Shift\+/i, "⇧")
+    .replace(/Cmd\+/i, "⌘");
+}
+
 // ─── Helpers ───────────────────────────────────────────────────────────────
 
 /** Extract the text after a heading at a given level, up to the next heading of same or higher level. */

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

@@ -42,6 +42,7 @@ const BASELINE_PATTERNS = [
   // ── GSD state directory (symlink to external storage) ──
   ".gsd",
   ".gsd-id",
+  ".bg-shell/",
 
   // ── OS junk ──
   ".DS_Store",

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

@@ -409,6 +409,7 @@ function initSchema(db: DbAdapter, fileBacked: boolean): void {
     db.exec("CREATE INDEX IF NOT EXISTS idx_milestones_status ON milestones(status)");
     db.exec("CREATE INDEX IF NOT EXISTS idx_quality_gates_pending ON quality_gates(milestone_id, slice_id, status)");
     db.exec("CREATE INDEX IF NOT EXISTS idx_verification_evidence_task ON verification_evidence(milestone_id, slice_id, task_id)");
+    db.exec("CREATE UNIQUE INDEX IF NOT EXISTS idx_verification_evidence_dedup ON verification_evidence(task_id, slice_id, milestone_id, command, verdict)");
 
     // v14 index — slice dependency lookups
     db.exec("CREATE INDEX IF NOT EXISTS idx_slice_deps_target ON slice_dependencies(milestone_id, depends_on_slice_id)");
@@ -450,6 +451,25 @@ function migrateSchema(db: DbAdapter): void {
   const currentVersion = row ? (row["v"] as number) : 0;
   if (currentVersion >= SCHEMA_VERSION) return;
 
+  // Backup database before migration so a mid-migration crash doesn't
+  // leave a partially-migrated DB with no recovery path.
+  // WAL-safe: checkpoint first to flush WAL into the main DB file, then copy.
+  if (currentPath && currentPath !== ":memory:" && existsSync(currentPath)) {
+    try {
+      const backupPath = `${currentPath}.backup-v${currentVersion}`;
+      if (!existsSync(backupPath)) {
+        // Flush WAL to main DB file before copying — without this, the backup
+        // may be missing committed data that only exists in the -wal file.
+        try { db.exec("PRAGMA wal_checkpoint(TRUNCATE)"); } catch { /* checkpoint is best-effort */ }
+        copyFileSync(currentPath, backupPath);
+      }
+    } catch (backupErr) {
+      // Log but proceed — blocking migration leaves the DB stuck at an old
+      // schema version permanently on read-only or full filesystems.
+      logWarning("db", `Pre-migration backup failed: ${backupErr instanceof Error ? backupErr.message : String(backupErr)}`);
+    }
+  }
+
   db.exec("BEGIN");
   try {
     if (currentVersion < 2) {
@@ -722,6 +742,7 @@ function migrateSchema(db: DbAdapter): void {
       db.exec("CREATE INDEX IF NOT EXISTS idx_milestones_status ON milestones(status)");
       db.exec("CREATE INDEX IF NOT EXISTS idx_quality_gates_pending ON quality_gates(milestone_id, slice_id, status)");
       db.exec("CREATE INDEX IF NOT EXISTS idx_verification_evidence_task ON verification_evidence(milestone_id, slice_id, task_id)");
+      db.exec("CREATE UNIQUE INDEX IF NOT EXISTS idx_verification_evidence_dedup ON verification_evidence(task_id, slice_id, milestone_id, command, verdict)");
       db.prepare("INSERT INTO schema_version (version, applied_at) VALUES (:version, :applied_at)").run({
         ":version": 13,
         ":applied_at": new Date().toISOString(),
@@ -997,9 +1018,21 @@ export function _resetProvider(): void {
 
 export function upsertDecision(d: Omit<Decision, "seq">): void {
   if (!currentDb) throw new GSDError(GSD_STALE_STATE, "gsd-db: No database open");
+  // Use ON CONFLICT DO UPDATE instead of INSERT OR REPLACE to preserve the
+  // seq column. INSERT OR REPLACE deletes then reinserts, resetting seq and
+  // corrupting decision ordering in DECISIONS.md after reconcile replay.
   currentDb.prepare(
-    `INSERT OR REPLACE INTO decisions (id, when_context, scope, decision, choice, rationale, revisable, made_by, superseded_by)
-     VALUES (:id, :when_context, :scope, :decision, :choice, :rationale, :revisable, :made_by, :superseded_by)`,
+    `INSERT INTO decisions (id, when_context, scope, decision, choice, rationale, revisable, made_by, superseded_by)
+     VALUES (:id, :when_context, :scope, :decision, :choice, :rationale, :revisable, :made_by, :superseded_by)
+     ON CONFLICT(id) DO UPDATE SET
+       when_context = excluded.when_context,
+       scope = excluded.scope,
+       decision = excluded.decision,
+       choice = excluded.choice,
+       rationale = excluded.rationale,
+       revisable = excluded.revisable,
+       made_by = excluded.made_by,
+       superseded_by = excluded.superseded_by`,
   ).run({
     ":id": d.id,
     ":when_context": d.when_context,
@@ -1119,7 +1152,9 @@ export function insertMilestone(m: {
   ).run({
     ":id": m.id,
     ":title": m.title ?? "",
-    ":status": m.status ?? "active",
+    // Default to "queued" — never auto-create milestones as "active" (#3380).
+    // Callers that need "active" must pass it explicitly.
+    ":status": m.status ?? "queued",
     ":depends_on": JSON.stringify(m.depends_on ?? []),
     ":created_at": new Date().toISOString(),
     ":vision": m.planning?.vision ?? "",
@@ -1349,6 +1384,13 @@ export function updateTaskStatus(milestoneId: string, sliceId: string, taskId: s
   });
 }
 
+export function setTaskBlockerDiscovered(milestoneId: string, sliceId: string, taskId: string, discovered: boolean): void {
+  if (!currentDb) return;
+  currentDb.prepare(
+    `UPDATE tasks SET blocker_discovered = :discovered WHERE milestone_id = :mid AND slice_id = :sid AND id = :tid`,
+  ).run({ ":discovered": discovered ? 1 : 0, ":mid": milestoneId, ":sid": sliceId, ":tid": taskId });
+}
+
 export function upsertTaskPlanning(milestoneId: string, sliceId: string, taskId: string, planning: Partial<TaskPlanningRecord>): void {
   if (!currentDb) throw new GSDError(GSD_STALE_STATE, "gsd-db: No database open");
   currentDb.prepare(
@@ -1543,7 +1585,7 @@ export function insertVerificationEvidence(e: {
 }): void {
   if (!currentDb) throw new GSDError(GSD_STALE_STATE, "gsd-db: No database open");
   currentDb.prepare(
-    `INSERT INTO verification_evidence (task_id, slice_id, milestone_id, command, exit_code, verdict, duration_ms, created_at)
+    `INSERT OR IGNORE INTO verification_evidence (task_id, slice_id, milestone_id, command, exit_code, verdict, duration_ms, created_at)
      VALUES (:task_id, :slice_id, :milestone_id, :command, :exit_code, :verdict, :duration_ms, :created_at)`,
   ).run({
     ":task_id": e.taskId,