fix(cli): require --confirm flag before phases clear deletes directories (#1832)

phases clear now checks for phase dirs before deleting. If any exist and
--confirm is absent, the command exits non-zero with a message showing the
count and how to proceed. Empty phases dir (nothing to delete) succeeds
without --confirm unchanged.

Updates new-milestone.md workflow to pass --confirm (intentional programmatic
caller). Updates existing new-milestone-clear-phases tests to match new API.

Closes #1826

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

tests/bug-1826-phases-clear-confirm.test.cjs

@@ -0,0 +1,72 @@
+/**
+ * Regression tests for bug #1826
+ *
+ * `phases clear` must require an explicit --confirm flag before deleting any
+ * phase directories. Without it, any accidental or hallucinated invocation
+ * wipes the entire .planning/phases/ tree with no warning.
+ *
+ * Rules:
+ *   - Phase dirs present + no --confirm → non-zero exit, clear error message
+ *   - Phase dirs present + --confirm    → deletes, exits 0, reports count
+ *   - No phase dirs + no --confirm      → exits 0, cleared=0 (nothing to guard)
+ */
+
+'use strict';
+
+const { describe, test, beforeEach, afterEach } = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('fs');
+const path = require('path');
+const { runGsdTools, createTempProject, cleanup } = require('./helpers.cjs');
+
+describe('bug #1826: phases clear --confirm guard', () => {
+  let tmpDir;
+
+  beforeEach(() => {
+    tmpDir = createTempProject();
+  });
+
+  afterEach(() => {
+    cleanup(tmpDir);
+  });
+
+  test('phases clear without --confirm is rejected when phase dirs exist', () => {
+    const phasesDir = path.join(tmpDir, '.planning', 'phases');
+    fs.mkdirSync(path.join(phasesDir, '01-foundation'), { recursive: true });
+    fs.mkdirSync(path.join(phasesDir, '02-api'), { recursive: true });
+
+    const result = runGsdTools(['phases', 'clear'], tmpDir);
+
+    assert.ok(!result.success, 'should exit non-zero when dirs exist and --confirm absent');
+    assert.ok(
+      result.error.includes('--confirm'),
+      `error message must mention --confirm; got: ${result.error}`
+    );
+
+    // Dirs must be untouched
+    assert.ok(fs.existsSync(path.join(phasesDir, '01-foundation')), 'dirs must not be deleted');
+    assert.ok(fs.existsSync(path.join(phasesDir, '02-api')), 'dirs must not be deleted');
+  });
+
+  test('phases clear --confirm deletes dirs and reports count', () => {
+    const phasesDir = path.join(tmpDir, '.planning', 'phases');
+    fs.mkdirSync(path.join(phasesDir, '01-foundation'), { recursive: true });
+    fs.mkdirSync(path.join(phasesDir, '02-api'), { recursive: true });
+
+    const result = runGsdTools(['phases', 'clear', '--confirm'], tmpDir);
+
+    assert.ok(result.success, `should succeed with --confirm: ${result.error}`);
+    const out = JSON.parse(result.output);
+    assert.strictEqual(out.cleared, 2);
+    assert.ok(!fs.existsSync(path.join(phasesDir, '01-foundation')), 'dirs should be removed');
+  });
+
+  test('phases clear without --confirm succeeds when no phase dirs exist', () => {
+    // .planning/phases/ exists but is empty — nothing to guard
+    const result = runGsdTools(['phases', 'clear'], tmpDir);
+
+    assert.ok(result.success, `should succeed with empty phases dir: ${result.error}`);
+    const out = JSON.parse(result.output);
+    assert.strictEqual(out.cleared, 0);
+  });
+});

tests/new-milestone-clear-phases.test.cjs

@@ -35,7 +35,7 @@ describe('phases clear command', () => {
     fs.writeFileSync(path.join(phase1, '01-01-PLAN.md'), '# Plan');
     fs.writeFileSync(path.join(phase2, '02-01-SUMMARY.md'), '# Summary');
 
-    const result = runGsdTools('phases clear', tmpDir);
+    const result = runGsdTools('phases clear --confirm', tmpDir);
     assert.ok(result.success, `Command failed: ${result.error}`);
 
     const output = JSON.parse(result.output);
@@ -54,7 +54,7 @@ describe('phases clear command', () => {
     const phasesDir = path.join(tmpDir, '.planning', 'phases');
     // createTempProject creates the directory but leaves it empty
 
-    const result = runGsdTools('phases clear', tmpDir);
+    const result = runGsdTools('phases clear --confirm', tmpDir);
     assert.ok(result.success, `Command failed: ${result.error}`);
 
     const output = JSON.parse(result.output);
@@ -66,7 +66,7 @@ describe('phases clear command', () => {
     // Remove the phases directory entirely
     fs.rmSync(path.join(tmpDir, '.planning', 'phases'), { recursive: true, force: true });
 
-    const result = runGsdTools('phases clear', tmpDir);
+    const result = runGsdTools('phases clear --confirm', tmpDir);
     assert.ok(result.success, `Command failed: ${result.error}`);
 
     const output = JSON.parse(result.output);
@@ -83,7 +83,7 @@ describe('phases clear command', () => {
     fs.mkdirSync(phase1, { recursive: true });
     fs.writeFileSync(path.join(phase1, '01-01-PLAN.md'), '# Plan');
 
-    const result = runGsdTools('phases clear', tmpDir);
+    const result = runGsdTools('phases clear --confirm', tmpDir);
     assert.ok(result.success, `Command failed: ${result.error}`);
 
     const output = JSON.parse(result.output);
@@ -103,7 +103,7 @@ describe('phases clear command', () => {
     fs.mkdirSync(nested, { recursive: true });
     fs.writeFileSync(path.join(nested, 'deep-file.md'), '# Deep');
 
-    const result = runGsdTools('phases clear', tmpDir);
+    const result = runGsdTools('phases clear --confirm', tmpDir);
     assert.ok(result.success, `Command failed: ${result.error}`);
 
     assert.ok(!fs.existsSync(phase1), 'phase directory including nested content should be removed');