fix(manager): address review — withProjectRoot, milestone filter, planningPaths

Fixes from trek-e's review on PR #1282:

1. Add missing withProjectRoot() wrapper on output — all other cmdInit*
   functions include project_root in JSON, manager was the only one without it.

2. Add getMilestonePhaseFilter() to directory scan — prevents stale phase
   directories from prior milestones appearing as phantom dashboard entries.

3. Replace hardcoded .planning/ paths with planningPaths(cwd) — forward
   compatibility with workstream scoping (#1268).

4. Add 3 new tests:
   - Conflict filter blocks dependent phase execution when dep is active
   - Conflict filter allows independent phase execution in parallel
   - Output includes project_root field

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

get-shit-done/bin/lib/init.cjs

@@ -5,7 +5,7 @@
 const fs = require('fs');
 const path = require('path');
 const { execSync } = require('child_process');
-const { loadConfig, resolveModelInternal, findPhaseInternal, getRoadmapPhaseInternal, pathExistsInternal, generateSlugInternal, getMilestoneInfo, getMilestonePhaseFilter, stripShippedMilestones, extractCurrentMilestone, normalizePhaseName, toPosixPath, output, error } = require('./core.cjs');
+const { loadConfig, resolveModelInternal, findPhaseInternal, getRoadmapPhaseInternal, pathExistsInternal, generateSlugInternal, getMilestoneInfo, getMilestonePhaseFilter, stripShippedMilestones, extractCurrentMilestone, normalizePhaseName, planningPaths, toPosixPath, output, error } = require('./core.cjs');
 
 function getLatestCompletedMilestone(cwd) {
   const milestonesPath = path.join(cwd, '.planning', 'MILESTONES.md');
@@ -765,19 +765,20 @@ function cmdInitManager(cwd, raw) {
   const config = loadConfig(cwd);
   const milestone = getMilestoneInfo(cwd);
 
+  // Use planningPaths for forward-compatibility with workstream scoping (#1268)
+  const paths = planningPaths(cwd);
+
   // Validate prerequisites
-  if (!pathExistsInternal(cwd, '.planning/ROADMAP.md')) {
+  if (!fs.existsSync(paths.roadmap)) {
     error('No ROADMAP.md found. Run /gsd:new-milestone first.');
   }
-  if (!pathExistsInternal(cwd, '.planning/STATE.md')) {
+  if (!fs.existsSync(paths.state)) {
     error('No STATE.md found. Run /gsd:new-milestone first.');
   }
-
+  const rawContent = fs.readFileSync(paths.roadmap, 'utf-8');
-  // Use roadmap analysis for rich phase data (depends_on, disk_status, has_context, etc.)
-  const roadmapPath = path.join(cwd, '.planning', 'ROADMAP.md');
-  const rawContent = fs.readFileSync(roadmapPath, 'utf-8');
   const content = extractCurrentMilestone(rawContent, cwd);
-  const phasesDir = path.join(cwd, '.planning', 'phases');
+  const phasesDir = paths.phases;
+  const isDirInMilestone = getMilestonePhaseFilter(cwd);
 
   const phasePattern = /#{2,4}\s*Phase\s+(\d+[A-Z]?(?:\.\d+)*)\s*:\s*([^\n]+)/gi;
   const phases = [];
@@ -810,7 +811,7 @@ function cmdInitManager(cwd, raw) {
 
     try {
       const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
-      const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
+      const dirs = entries.filter(e => e.isDirectory()).map(e => e.name).filter(isDirInMilestone);
       const dirMatch = dirs.find(d => d.startsWith(normalized + '-') || d === normalized);
 
       if (dirMatch) {
@@ -1004,7 +1005,7 @@ function cmdInitManager(cwd, raw) {
     state_exists: true,
   };
 
-  output(result, raw);
+  output(withProjectRoot(cwd, result), raw);
 }
 
 function cmdInitProgress(cwd, raw) {

tests/init-manager.test.cjs

@@ -358,4 +358,59 @@ describe('init manager', () => {
     assert.strictEqual(output.phases[0].is_active, true);
     assert.ok(output.phases[0].last_activity !== null);
   });
+
+  test('conflict filter: blocks dependent phase execute when dep is active', () => {
+    writeState(tmpDir);
+    writeRoadmap(tmpDir, [
+      { number: '1', name: 'Foundation', complete: true },
+      { number: '2', name: 'API Layer', depends_on: 'Phase 1' },
+      { number: '3', name: 'Auth', depends_on: 'Phase 2' },
+    ]);
+
+    // Phase 2: partial (actively executing — has 2 plans, 1 summary)
+    scaffoldPhase(tmpDir, 2, { slug: 'api-layer', context: true, plans: 2, summaries: 1 });
+    // Phase 3: planned and deps would be met if Phase 2 were complete, but it's not
+    scaffoldPhase(tmpDir, 3, { slug: 'auth', context: true, plans: 1 });
+
+    const result = runGsdTools('init manager', tmpDir);
+    const output = JSON.parse(result.output);
+
+    // Phase 2 is partial — should NOT appear as execute recommendation (already running)
+    // Phase 3 deps_satisfied is false (Phase 2 not complete) — also no recommendation
+    const execRecs = output.recommended_actions.filter(r => r.action === 'execute');
+    assert.strictEqual(execRecs.length, 0);
+  });
+
+  test('conflict filter: allows independent phase execute in parallel', () => {
+    writeState(tmpDir);
+    writeRoadmap(tmpDir, [
+      { number: '1', name: 'Foundation', complete: true },
+      { number: '2', name: 'API Layer', depends_on: 'Phase 1' },
+      { number: '3', name: 'Notifications' }, // no deps — independent
+    ]);
+
+    // Phase 2: partial (actively executing)
+    scaffoldPhase(tmpDir, 2, { slug: 'api-layer', context: true, plans: 2, summaries: 1 });
+    // Phase 3: planned, no deps — independent of Phase 2
+    scaffoldPhase(tmpDir, 3, { slug: 'notifications', context: true, plans: 1 });
+
+    const result = runGsdTools('init manager', tmpDir);
+    const output = JSON.parse(result.output);
+
+    // Phase 3 is independent of Phase 2 — should be recommended for execution
+    const execRecs = output.recommended_actions.filter(r => r.action === 'execute');
+    assert.strictEqual(execRecs.length, 1);
+    assert.strictEqual(execRecs[0].phase, '3');
+  });
+
+  test('output includes project_root field', () => {
+    writeState(tmpDir);
+    writeRoadmap(tmpDir, [{ number: '1', name: 'Test' }]);
+
+    const result = runGsdTools('init manager', tmpDir);
+    const output = JSON.parse(result.output);
+
+    // macOS resolves /var → /private/var; normalize both sides
+    assert.strictEqual(fs.realpathSync(output.project_root), fs.realpathSync(tmpDir));
+  });
 });