gsd-pi 2.43.0 → 2.44.0-dev.62b5d6c

package/dist/resources/extensions/gsd/bootstrap/dynamic-tools.js

@@ -1,16 +1,41 @@
 import { existsSync } from "node:fs";
-import { join } from "node:path";
+import { join, sep } from "node:path";
 import { createBashTool, createEditTool, createReadTool, createWriteTool } from "@gsd/pi-coding-agent";
 import { DEFAULT_BASH_TIMEOUT_SECS } from "../constants.js";
+/**
+ * Resolve the correct DB path for the current working directory.
+ * If `basePath` is inside a `.gsd/worktrees/<MID>/` directory, returns
+ * the project root's `.gsd/gsd.db` (shared WAL — R012). Otherwise
+ * returns `<basePath>/.gsd/gsd.db`.
+ */
+export function resolveProjectRootDbPath(basePath) {
+    // Detect worktree: look for `.gsd/worktrees/` in the path segments.
+    // A worktree path looks like: /project/root/.gsd/worktrees/M001/...
+    // We need to resolve back to /project/root/.gsd/gsd.db
+    const marker = `${sep}.gsd${sep}worktrees${sep}`;
+    const idx = basePath.indexOf(marker);
+    if (idx !== -1) {
+        const projectRoot = basePath.slice(0, idx);
+        return join(projectRoot, ".gsd", "gsd.db");
+    }
+    // Also handle forward-slash paths on all platforms
+    const fwdMarker = "/.gsd/worktrees/";
+    const fwdIdx = basePath.indexOf(fwdMarker);
+    if (fwdIdx !== -1) {
+        const projectRoot = basePath.slice(0, fwdIdx);
+        return join(projectRoot, ".gsd", "gsd.db");
+    }
+    return join(basePath, ".gsd", "gsd.db");
+}
 export async function ensureDbOpen() {
     try {
         const db = await import("../gsd-db.js");
         if (db.isDbAvailable())
             return true;
         const basePath = process.cwd();
+        const dbPath = resolveProjectRootDbPath(basePath);
         const gsdDir = join(basePath, ".gsd");
-        const dbPath = join(gsdDir, "gsd.db");
-        // Open existing DB file
+        // Open existing DB file (may be at project root for worktrees)
         if (existsSync(dbPath)) {
             return db.openDatabase(dbPath);
         }

package/dist/resources/extensions/gsd/bootstrap/register-hooks.js

@@ -24,6 +24,13 @@ export function registerHooks(pi) {
         resetWriteGateState();
         resetToolCallLoopGuard();
         await syncServiceTierStatus(ctx);
+        // Apply show_token_cost preference (#1515)
+        try {
+            const { loadEffectiveGSDPreferences } = await import("../preferences.js");
+            const prefs = loadEffectiveGSDPreferences();
+            process.env.GSD_SHOW_TOKEN_COST = prefs?.preferences.show_token_cost ? "1" : "";
+        }
+        catch { /* non-fatal */ }
         if (isFirstSession) {
             isFirstSession = false;
         }

package/dist/resources/extensions/gsd/commands/catalog.js

@@ -4,7 +4,7 @@ import { join } from "node:path";
 import { loadRegistry } from "../workflow-templates.js";
 import { resolveProjectRoot } from "../worktree.js";
 const gsdHome = process.env.GSD_HOME || join(homedir(), ".gsd");
-export const GSD_COMMAND_DESCRIPTION = "GSD — Get Shit Done: /gsd help|start|templates|next|auto|stop|pause|status|widget|visualize|queue|quick|discuss|capture|triage|dispatch|history|undo|rate|skip|export|cleanup|mode|prefs|config|keys|hooks|run-hook|skill-health|doctor|logs|forensics|changelog|migrate|remote|steer|knowledge|new-milestone|parallel|cmux|park|unpark|init|setup|inspect|extensions|update|fast";
+export const GSD_COMMAND_DESCRIPTION = "GSD — Get Shit Done: /gsd help|start|templates|next|auto|stop|pause|status|widget|visualize|queue|quick|discuss|capture|triage|dispatch|history|undo|undo-task|reset-slice|rate|skip|export|cleanup|mode|prefs|config|keys|hooks|run-hook|skill-health|doctor|logs|forensics|changelog|migrate|remote|steer|knowledge|new-milestone|parallel|cmux|park|unpark|init|setup|inspect|extensions|update|fast";
 export const TOP_LEVEL_SUBCOMMANDS = [
     { cmd: "help", desc: "Categorized command reference with descriptions" },
     { cmd: "next", desc: "Explicit step mode (same as /gsd)" },
@@ -23,6 +23,8 @@ export const TOP_LEVEL_SUBCOMMANDS = [
     { cmd: "dispatch", desc: "Dispatch a specific phase directly" },
     { cmd: "history", desc: "View execution history" },
     { cmd: "undo", desc: "Revert last completed unit" },
+    { cmd: "undo-task", desc: "Reset a specific task's completion state (DB + markdown)" },
+    { cmd: "reset-slice", desc: "Reset a slice and all its tasks (DB + markdown)" },
     { cmd: "rate", desc: "Rate last unit's model tier (over/ok/under) — improves adaptive routing" },
     { cmd: "skip", desc: "Prevent a unit from auto-mode dispatch" },
     { cmd: "export", desc: "Export milestone/slice results" },

package/dist/resources/extensions/gsd/commands/handlers/ops.js

@@ -3,7 +3,7 @@ import { handleConfig } from "../../commands-config.js";
 import { handleDoctor, handleCapture, handleKnowledge, handleRunHook, handleSkillHealth, handleSteer, handleTriage, handleUpdate } from "../../commands-handlers.js";
 import { handleInspect } from "../../commands-inspect.js";
 import { handleLogs } from "../../commands-logs.js";
-import { handleCleanupBranches, handleCleanupSnapshots, handleSkip, handleCleanupProjects, handleCleanupWorktrees } from "../../commands-maintenance.js";
+import { handleCleanupBranches, handleCleanupSnapshots, handleSkip, handleCleanupProjects, handleCleanupWorktrees, handleRecover } from "../../commands-maintenance.js";
 import { handleExport } from "../../export.js";
 import { handleHistory } from "../../history.js";
 import { handleUndo } from "../../undo.js";
@@ -50,6 +50,16 @@ export async function handleOpsCommand(trimmed, ctx, pi) {
         await handleHistory(trimmed.replace(/^history\s*/, "").trim(), ctx, projectRoot());
         return true;
     }
+    if (trimmed === "undo-task" || trimmed.startsWith("undo-task ")) {
+        const { handleUndoTask } = await import("../../undo.js");
+        await handleUndoTask(trimmed.replace(/^undo-task\s*/, "").trim(), ctx, pi, projectRoot());
+        return true;
+    }
+    if (trimmed === "reset-slice" || trimmed.startsWith("reset-slice ")) {
+        const { handleResetSlice } = await import("../../undo.js");
+        await handleResetSlice(trimmed.replace(/^reset-slice\s*/, "").trim(), ctx, pi, projectRoot());
+        return true;
+    }
     if (trimmed === "undo" || trimmed.startsWith("undo ")) {
         await handleUndo(trimmed.replace(/^undo\s*/, "").trim(), ctx, pi, projectRoot());
         return true;
@@ -62,6 +72,10 @@ export async function handleOpsCommand(trimmed, ctx, pi) {
         await handleSkip(trimmed.replace(/^skip\s*/, "").trim(), ctx, projectRoot());
         return true;
     }
+    if (trimmed === "recover") {
+        await handleRecover(ctx, projectRoot());
+        return true;
+    }
     if (trimmed === "export" || trimmed.startsWith("export ")) {
         await handleExport(trimmed.replace(/^export\s*/, "").trim(), ctx, projectRoot());
         return true;

package/dist/resources/extensions/gsd/commands-handlers.js

@@ -62,7 +62,7 @@ export async function handleDoctor(args, ctx, pi) {
             scope: effectiveScope,
             includeWarnings: true,
         });
-        const actionable = unresolved.filter(issue => issue.severity === "error" || issue.code === "all_tasks_done_missing_slice_uat" || issue.code === "slice_checked_missing_uat");
+        const actionable = unresolved.filter(issue => issue.severity === "error");
         if (actionable.length === 0) {
             ctx.ui.notify("Doctor heal found nothing actionable to hand off to the LLM.", "info");
             return;

package/dist/resources/extensions/gsd/commands-maintenance.js

@@ -1,7 +1,7 @@
 /**
- * GSD Maintenance — cleanup, skip, and dry-run handlers.
+ * GSD Maintenance — cleanup, skip, dry-run, and recover handlers.
  *
- * Contains: handleCleanupBranches, handleCleanupSnapshots, handleCleanupWorktrees, handleSkip, handleDryRun
+ * Contains: handleCleanupBranches, handleCleanupSnapshots, handleCleanupWorktrees, handleSkip, handleDryRun, handleRecover
  */
 import { deriveState } from "./state.js";
 import { nativeBranchList, nativeDetectMainBranch, nativeBranchListMerged, nativeBranchDelete, nativeForEachRef, nativeUpdateRef } from "./native-git-bridge.js";
@@ -40,14 +40,32 @@ export async function handleCleanupBranches(ctx, basePath) {
     try {
         const { listWorktrees } = await import("./worktree-manager.js");
         const { resolveMilestoneFile } = await import("./paths.js");
-        const { loadFile, parseRoadmap } = await import("./files.js");
+        const { loadFile } = await import("./files.js");
+        const { parseRoadmap } = await import("./parsers-legacy.js");
         const { isMilestoneComplete } = await import("./state.js");
+        const { isDbAvailable, getMilestone } = await import("./gsd-db.js");
         const attachedBranches = new Set(listWorktrees(basePath).map((wt) => wt.branch));
         const milestoneBranches = nativeBranchList(basePath, "milestone/*");
         for (const branch of milestoneBranches) {
             if (attachedBranches.has(branch))
                 continue;
             const milestoneId = branch.replace(/^milestone\//, "");
+            // DB-first: check milestone status directly
+            if (isDbAvailable()) {
+                const dbRow = getMilestone(milestoneId);
+                if (dbRow) {
+                    if (dbRow.status !== "complete" && dbRow.status !== "done")
+                        continue;
+                    // Milestone is complete per DB — proceed to delete branch
+                    try {
+                        nativeBranchDelete(basePath, branch, true);
+                        deletedStaleMilestones++;
+                    }
+                    catch { /* non-fatal */ }
+                    continue;
+                }
+            }
+            // Filesystem fallback
             const roadmapPath = resolveMilestoneFile(basePath, milestoneId, "ROADMAP");
             if (!roadmapPath)
                 continue;
@@ -408,3 +426,60 @@ export async function handleCleanupProjects(args, ctx) {
     }
     ctx.ui.notify(lines.join("\n"), "info");
 }
+/**
+ * `gsd recover` — Reconstruct DB hierarchy state from rendered markdown on disk.
+ *
+ * Deletes milestones, slices, and tasks table rows (preserves decisions,
+ * requirements, artifacts, memories), re-runs `migrateHierarchyToDb()` to
+ * repopulate from markdown, then calls `deriveState()` to verify sanity.
+ *
+ * Prints counts of recovered items and the resulting project phase.
+ */
+export async function handleRecover(ctx, basePath) {
+    const { isDbAvailable: dbAvailable, _getAdapter, transaction: dbTransaction } = await import("./gsd-db.js");
+    const { migrateHierarchyToDb } = await import("./md-importer.js");
+    const { invalidateStateCache } = await import("./state.js");
+    if (!dbAvailable()) {
+        ctx.ui.notify("gsd recover: No database open. Run a GSD command first to initialize the DB.", "error");
+        return;
+    }
+    try {
+        // 1. Delete + re-populate inside a single transaction for atomicity
+        const db = _getAdapter();
+        const counts = dbTransaction(() => {
+            db.exec("DELETE FROM tasks");
+            db.exec("DELETE FROM slices");
+            db.exec("DELETE FROM milestones");
+            return migrateHierarchyToDb(basePath);
+        });
+        // 3. Invalidate state cache so deriveState() picks up fresh DB data
+        invalidateStateCache();
+        // 4. Derive state to verify sanity
+        const state = await deriveState(basePath);
+        // 5. Report
+        const lines = [
+            `gsd recover: reconstructed hierarchy from markdown`,
+            `  Milestones: ${counts.milestones}`,
+            `  Slices:     ${counts.slices}`,
+            `  Tasks:      ${counts.tasks}`,
+            ``,
+            `  Phase:      ${state.phase}`,
+        ];
+        if (state.activeMilestone) {
+            lines.push(`  Active:     ${state.activeMilestone.id}: ${state.activeMilestone.title}`);
+        }
+        if (state.activeSlice) {
+            lines.push(`  Slice:      ${state.activeSlice.id}: ${state.activeSlice.title}`);
+        }
+        if (state.activeTask) {
+            lines.push(`  Task:       ${state.activeTask.id}: ${state.activeTask.title}`);
+        }
+        process.stderr.write(`gsd-recover: recovered ${counts.milestones}M/${counts.slices}S/${counts.tasks}T hierarchy\n`);
+        ctx.ui.notify(lines.join("\n"), "success");
+    }
+    catch (err) {
+        const msg = err instanceof Error ? err.message : String(err);
+        process.stderr.write(`gsd-recover: failed: ${msg}\n`);
+        ctx.ui.notify(`gsd recover failed: ${msg}`, "error");
+    }
+}

package/dist/resources/extensions/gsd/dashboard-overlay.js

@@ -7,8 +7,9 @@
  */
 import { truncateToWidth, visibleWidth, matchesKey, Key } from "@gsd/pi-tui";
 import { deriveState } from "./state.js";
-import { loadFile, parseRoadmap, parsePlan } from "./files.js";
-import { resolveMilestoneFile, resolveSliceFile } from "./paths.js";
+import { loadFile } from "./files.js";
+import { isDbAvailable, getMilestoneSlices, getSliceTasks } from "./gsd-db.js";
+import { resolveMilestoneFile } from "./paths.js";
 import { getAutoDashboardData } from "./auto.js";
 import { getLedger, getProjectTotals, aggregateByPhase, aggregateBySlice, aggregateByModel, aggregateCacheHitRate, formatCost, formatTokenCount, formatCostProjection, } from "./metrics.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
@@ -136,38 +137,38 @@ export class GSDDashboardOverlay {
             };
             const roadmapFile = resolveMilestoneFile(base, mid, "ROADMAP");
             const roadmapContent = roadmapFile ? await loadFile(roadmapFile) : null;
-            if (roadmapContent) {
-                const roadmap = parseRoadmap(roadmapContent);
-                for (const s of roadmap.slices) {
-                    const sliceView = {
-                        id: s.id,
-                        title: s.title,
-                        done: s.done,
-                        risk: s.risk,
-                        active: state.activeSlice?.id === s.id,
-                        tasks: [],
-                    };
-                    if (sliceView.active) {
-                        const planFile = resolveSliceFile(base, mid, s.id, "PLAN");
-                        const planContent = planFile ? await loadFile(planFile) : null;
-                        if (planContent) {
-                            const plan = parsePlan(planContent);
-                            sliceView.taskProgress = {
-                                done: plan.tasks.filter(t => t.done).length,
-                                total: plan.tasks.length,
-                            };
-                            for (const t of plan.tasks) {
-                                sliceView.tasks.push({
-                                    id: t.id,
-                                    title: t.title,
-                                    done: t.done,
-                                    active: state.activeTask?.id === t.id,
-                                });
-                            }
+            let normSlices = [];
+            if (isDbAvailable()) {
+                normSlices = getMilestoneSlices(mid).map(s => ({ id: s.id, done: s.status === "complete", title: s.title, risk: s.risk || "medium" }));
+            }
+            for (const s of normSlices) {
+                const sliceView = {
+                    id: s.id,
+                    title: s.title,
+                    done: s.done,
+                    risk: s.risk,
+                    active: state.activeSlice?.id === s.id,
+                    tasks: [],
+                };
+                if (sliceView.active) {
+                    // Normalize tasks from DB
+                    if (isDbAvailable()) {
+                        const dbTasks = getSliceTasks(mid, s.id);
+                        sliceView.taskProgress = {
+                            done: dbTasks.filter(t => t.status === "complete" || t.status === "done").length,
+                            total: dbTasks.length,
+                        };
+                        for (const t of dbTasks) {
+                            sliceView.tasks.push({
+                                id: t.id,
+                                title: t.title,
+                                done: t.status === "complete" || t.status === "done",
+                                active: state.activeTask?.id === t.id,
+                            });
                         }
                     }
-                    view.slices.push(sliceView);
                 }
+                view.slices.push(sliceView);
             }
             this.milestoneData = view;
             return true;

package/dist/resources/extensions/gsd/db-writer.js

@@ -8,12 +8,60 @@
 // Critical invariant: generated markdown must round-trip through
 // parseDecisionsTable() and parseRequirementsSections() with field fidelity.
 import { resolve } from 'node:path';
+import { readFileSync, existsSync } from 'node:fs';
 import { resolveGsdRootFile } from './paths.js';
 import { saveFile } from './files.js';
 import { GSDError, GSD_STALE_STATE, GSD_IO_ERROR } from './errors.js';
 import { invalidateStateCache } from './state.js';
 import { clearPathCache } from './paths.js';
 import { clearParseCache } from './files.js';
+// ─── Freeform Detection ───────────────────────────────────────────────────
+/**
+ * Detect whether a DECISIONS.md file is in canonical table format
+ * (generated by generateDecisionsMd).
+ *
+ * Returns true only if the file starts with the canonical header
+ * ("# Decisions Register") that generateDecisionsMd produces.
+ * Files with freeform content — even if they contain an appended
+ * decisions table section — return false so the freeform content
+ * is preserved.
+ */
+export function isDecisionsTableFormat(content) {
+    // The canonical format always starts with "# Decisions Register"
+    const firstLine = content.split('\n')[0]?.trim() ?? '';
+    if (firstLine !== '# Decisions Register')
+        return false;
+    // Additionally verify the file has the canonical table header
+    return content.includes('| # | When | Scope | Decision | Choice | Rationale | Revisable?');
+}
+/**
+ * Generate a minimal decisions table section (header + rows) for appending
+ * to a freeform DECISIONS.md file.
+ */
+function generateDecisionsAppendBlock(decisions) {
+    const lines = [];
+    lines.push('');
+    lines.push('---');
+    lines.push('');
+    lines.push('## Decisions Table');
+    lines.push('');
+    lines.push('| # | When | Scope | Decision | Choice | Rationale | Revisable? | Made By |');
+    lines.push('|---|------|-------|----------|--------|-----------|------------|---------|');
+    for (const d of decisions) {
+        const cells = [
+            d.id,
+            d.when_context,
+            d.scope,
+            d.decision,
+            d.choice,
+            d.rationale,
+            d.revisable,
+            d.made_by ?? 'agent',
+        ].map(cell => (cell ?? '').replace(/\|/g, '\\|'));
+        lines.push(`| ${cells.join(' | ')} |`);
+    }
+    return lines.join('\n') + '\n';
+}
 // ─── Markdown Generators ──────────────────────────────────────────────────
 /**
  * Generate full DECISIONS.md content from an array of Decision objects.
@@ -194,9 +242,37 @@ export async function saveDecisionToDb(fields, basePath) {
                 superseded_by: row['superseded_by'] ?? null,
             }));
         }
-        const md = generateDecisionsMd(allDecisions);
         const filePath = resolveGsdRootFile(basePath, 'DECISIONS');
-        await saveFile(filePath, md);
+        // Check if existing DECISIONS.md has freeform (non-table) content.
+        // If so, preserve that content and append/update the decisions table
+        // at the end instead of overwriting the entire file.
+        let existingContent = null;
+        if (existsSync(filePath)) {
+            existingContent = readFileSync(filePath, 'utf-8');
+        }
+        let md;
+        if (existingContent && !isDecisionsTableFormat(existingContent)) {
+            // Freeform content detected — preserve it and append decisions table.
+            // Strip any previously appended decisions table section to avoid duplication.
+            const marker = '---\n\n## Decisions Table';
+            const markerIdx = existingContent.indexOf(marker);
+            const freeformPart = markerIdx >= 0
+                ? existingContent.substring(0, markerIdx).trimEnd()
+                : existingContent.trimEnd();
+            md = freeformPart + '\n' + generateDecisionsAppendBlock(allDecisions);
+        }
+        else {
+            // Table format or no existing file — full regeneration (original behavior)
+            md = generateDecisionsMd(allDecisions);
+        }
+        try {
+            await saveFile(filePath, md);
+        }
+        catch (diskErr) {
+            process.stderr.write(`gsd-db: saveDecisionToDb — disk write failed, rolling back DB row: ${diskErr.message}\n`);
+            adapter?.prepare('DELETE FROM decisions WHERE id = :id').run({ ':id': id });
+            throw diskErr;
+        }
         // Invalidate file-read caches so deriveState() sees the updated markdown.
         // Do NOT clear the artifacts table — we just wrote to it intentionally.
         invalidateStateCache();
@@ -253,7 +329,14 @@ export async function updateRequirementInDb(id, updates, basePath) {
         const nonSuperseded = allRequirements.filter(r => r.superseded_by == null);
         const md = generateRequirementsMd(nonSuperseded);
         const filePath = resolveGsdRootFile(basePath, 'REQUIREMENTS');
-        await saveFile(filePath, md);
+        try {
+            await saveFile(filePath, md);
+        }
+        catch (diskErr) {
+            process.stderr.write(`gsd-db: updateRequirementInDb — disk write failed, reverting DB row: ${diskErr.message}\n`);
+            db.upsertRequirement(existing);
+            throw diskErr;
+        }
         // Invalidate file-read caches so deriveState() sees the updated markdown.
         // Do NOT clear the artifacts table — we just wrote to it intentionally.
         invalidateStateCache();
@@ -287,7 +370,15 @@ export async function saveArtifactToDb(opts, basePath) {
         if (!fullPath.startsWith(gsdDir)) {
             throw new GSDError(GSD_IO_ERROR, `saveArtifactToDb: path escapes .gsd/ directory: ${opts.path}`);
         }
-        await saveFile(fullPath, opts.content);
+        try {
+            await saveFile(fullPath, opts.content);
+        }
+        catch (diskErr) {
+            process.stderr.write(`gsd-db: saveArtifactToDb — disk write failed, rolling back DB row: ${diskErr.message}\n`);
+            const rollbackAdapter = db._getAdapter();
+            rollbackAdapter?.prepare('DELETE FROM artifacts WHERE path = :path').run({ ':path': opts.path });
+            throw diskErr;
+        }
         // Invalidate file-read caches so deriveState() sees the updated markdown.
         // Do NOT clear the artifacts table — we just wrote to it intentionally.
         invalidateStateCache();

package/dist/resources/extensions/gsd/dispatch-guard.js

@@ -1,8 +1,9 @@
 // GSD Dispatch Guard — prevents out-of-order slice dispatch
-import { readFileSync } from "node:fs";
 import { resolveMilestoneFile } from "./paths.js";
-import { parseRoadmapSlices } from "./roadmap-slices.js";
 import { findMilestoneIds } from "./guided-flow.js";
+import { isDbAvailable, getMilestoneSlices } from "./gsd-db.js";
+import { parseRoadmap } from "./parsers-legacy.js";
+import { readFileSync } from "node:fs";
 const SLICE_DISPATCH_TYPES = new Set([
     "research-slice",
     "plan-slice",
@@ -10,29 +11,6 @@ const SLICE_DISPATCH_TYPES = new Set([
     "execute-task",
     "complete-slice",
 ]);
-/**
- * Read a roadmap file from disk (working tree) rather than from a git branch.
- *
- * Prior implementation used `git show <branch>:<path>` which read committed
- * state on a specific branch. This caused false-positive blockers when work
- * was committed on a milestone/worktree branch but the integration branch
- * (main) hadn't been updated yet — the guard would see prior slices as
- * incomplete on main even though they were done in the working tree (#530).
- *
- * Reading from disk always reflects the latest state, regardless of which
- * branch is checked out or whether changes have been committed.
- */
-function readRoadmapFromDisk(base, milestoneId) {
-    try {
-        const absPath = resolveMilestoneFile(base, milestoneId, "ROADMAP");
-        if (!absPath)
-            return null;
-        return readFileSync(absPath, "utf-8").trim();
-    }
-    catch {
-        return null;
-    }
-}
 export function getPriorSliceCompletionBlocker(base, _mainBranch, unitType, unitId) {
     if (!SLICE_DISPATCH_TYPES.has(unitType))
         return null;
@@ -51,11 +29,38 @@ export function getPriorSliceCompletionBlocker(base, _mainBranch, unitType, unit
             continue;
         if (resolveMilestoneFile(base, mid, "SUMMARY"))
             continue;
-        // Read from disk (working tree) — always has the latest state
-        const roadmapContent = readRoadmapFromDisk(base, mid);
-        if (!roadmapContent)
-            continue;
-        const slices = parseRoadmapSlices(roadmapContent);
+        let slices = null;
+        if (isDbAvailable()) {
+            const rows = getMilestoneSlices(mid);
+            if (rows.length > 0) {
+                slices = rows.map((r) => ({
+                    id: r.id,
+                    done: r.status === "complete",
+                    depends: r.depends ?? [],
+                }));
+            }
+        }
+        if (!slices) {
+            // File-based fallback: parse roadmap checkboxes
+            const roadmapPath = resolveMilestoneFile(base, mid, "ROADMAP");
+            if (!roadmapPath)
+                continue;
+            let roadmapContent;
+            try {
+                roadmapContent = readFileSync(roadmapPath, "utf-8");
+            }
+            catch {
+                continue;
+            }
+            const parsed = parseRoadmap(roadmapContent);
+            if (parsed.slices.length === 0)
+                continue;
+            slices = parsed.slices.map((s) => ({
+                id: s.id,
+                done: s.done,
+                depends: s.depends ?? [],
+            }));
+        }
         if (mid !== targetMid) {
             const incomplete = slices.find((slice) => !slice.done);
             if (incomplete) {

package/dist/resources/extensions/gsd/doctor-checks.js

@@ -1,7 +1,9 @@
 import { existsSync, lstatSync, readdirSync, readFileSync, realpathSync, rmSync, statSync } from "node:fs";
 import { basename, dirname, join, sep } from "node:path";
 import { readRepoMeta, externalProjectsRoot, cleanNumberedGsdVariants } from "./repo-identity.js";
-import { loadFile, parseRoadmap } from "./files.js";
+import { loadFile } from "./files.js";
+import { parseRoadmap as parseLegacyRoadmap } from "./parsers-legacy.js";
+import { isDbAvailable, getMilestoneSlices } from "./gsd-db.js";
 import { resolveMilestoneFile, milestonesDir, gsdRoot, resolveGsdRootFile } from "./paths.js";
 import { deriveState, isMilestoneComplete } from "./state.js";
 import { saveFile } from "./files.js";
@@ -37,12 +39,19 @@ export async function checkGitHealth(basePath, issues, fixesApplied, shouldFix,
                 // Check if milestone is complete via roadmap
                 let isComplete = false;
                 if (milestoneEntry) {
-                    const roadmapPath = resolveMilestoneFile(basePath, milestoneId, "ROADMAP");
-                    const roadmapContent = roadmapPath ? await loadFile(roadmapPath) : null;
-                    if (roadmapContent) {
-                        const roadmap = parseRoadmap(roadmapContent);
-                        isComplete = isMilestoneComplete(roadmap);
+                    if (isDbAvailable()) {
+                        const dbSlices = getMilestoneSlices(milestoneId);
+                        isComplete = dbSlices.length > 0 && dbSlices.every(s => s.status === "complete");
                     }
+                    else {
+                        const roadmapPath = resolveMilestoneFile(basePath, milestoneId, "ROADMAP");
+                        const roadmapContent = roadmapPath ? await loadFile(roadmapPath) : null;
+                        if (roadmapContent) {
+                            const roadmap = parseLegacyRoadmap(roadmapContent);
+                            isComplete = isMilestoneComplete(roadmap);
+                        }
+                    }
+                    // When DB unavailable and no roadmap, isComplete stays false
                 }
                 if (isComplete) {
                     issues.push({
@@ -82,11 +91,19 @@ export async function checkGitHealth(basePath, issues, fixesApplied, shouldFix,
                             continue;
                         const milestoneId = branch.replace(/^milestone\//, "");
                         const roadmapPath = resolveMilestoneFile(basePath, milestoneId, "ROADMAP");
-                        const roadmapContent = roadmapPath ? await loadFile(roadmapPath) : null;
-                        if (!roadmapContent)
-                            continue;
-                        const roadmap = parseRoadmap(roadmapContent);
-                        if (isMilestoneComplete(roadmap)) {
+                        let branchMilestoneComplete = false;
+                        if (isDbAvailable()) {
+                            const dbSlices = getMilestoneSlices(milestoneId);
+                            branchMilestoneComplete = dbSlices.length > 0 && dbSlices.every(s => s.status === "complete");
+                        }
+                        else {
+                            const roadmapContent = roadmapPath ? await loadFile(roadmapPath) : null;
+                            if (!roadmapContent)
+                                continue;
+                            const roadmap = parseLegacyRoadmap(roadmapContent);
+                            branchMilestoneComplete = isMilestoneComplete(roadmap);
+                        }
+                        if (branchMilestoneComplete) {
                             issues.push({
                                 severity: "info",
                                 code: "stale_milestone_branch",

package/dist/resources/extensions/gsd/doctor-environment.js

@@ -19,6 +19,27 @@ const MIN_DISK_BYTES = 500 * 1024 * 1024;
 /** Timeout for external commands (ms). */
 const CMD_TIMEOUT = 5_000;
 // ── Helpers ────────────────────────────────────────────────────────────────
+/** Worktree sentinel — path segment that marks an auto-worktree directory. */
+const WORKTREE_PATH_SEGMENT = `${join(".gsd", "worktrees")}/`;
+/**
+ * Resolve the project root when running inside a `.gsd/worktrees/<name>/`
+ * auto-worktree. Returns `null` if not in a worktree.
+ *
+ * Detection order:
+ *   1. `GSD_WORKTREE` env var (set by the worktree launcher)
+ *   2. `.gsd/worktrees/` segment in basePath
+ */
+function resolveWorktreeProjectRoot(basePath) {
+    const envRoot = process.env.GSD_WORKTREE;
+    if (envRoot)
+        return envRoot;
+    const normalised = basePath.replace(/\\/g, "/");
+    const idx = normalised.indexOf(WORKTREE_PATH_SEGMENT.replace(/\\/g, "/"));
+    if (idx === -1)
+        return null;
+    // Everything before `.gsd/worktrees/` is the project root
+    return basePath.slice(0, idx);
+}
 function tryExec(cmd, cwd) {
     try {
         return execSync(cmd, {
@@ -87,6 +108,13 @@ function checkDependenciesInstalled(basePath) {
         return null;
     const nodeModules = join(basePath, "node_modules");
     if (!existsSync(nodeModules)) {
+        // In auto-worktrees node_modules is absent by design — the worktree
+        // symlinks to (or expects) the project root's copy.  Fall back to
+        // checking the project root before reporting an error (#2303).
+        const projectRoot = resolveWorktreeProjectRoot(basePath);
+        if (projectRoot && existsSync(join(projectRoot, "node_modules"))) {
+            return { name: "dependencies", status: "ok", message: "Dependencies installed (project root)" };
+        }
         return {
             name: "dependencies",
             status: "error",