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>

get-shit-done/bin/gsd-tools.cjs

@@ -602,7 +602,7 @@ async function runCommand(command, args, cwd, raw) {
         };
         phase.cmdPhasesList(cwd, options, raw);
       } else if (subcommand === 'clear') {
-        milestone.cmdPhasesClear(cwd, raw);
+        milestone.cmdPhasesClear(cwd, raw, args.slice(2));
       } else {
         error('Unknown phases subcommand. Available: list, clear');
       }

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

@@ -246,15 +246,24 @@ function cmdMilestoneComplete(cwd, version, options, raw) {
   output(result, raw);
 }
 
-function cmdPhasesClear(cwd, raw) {
+function cmdPhasesClear(cwd, raw, args) {
   const phasesDir = planningPaths(cwd).phases;
+  const confirm = Array.isArray(args) && args.includes('--confirm');
   let cleared = 0;
 
   if (fs.existsSync(phasesDir)) {
+    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+    const dirs = entries.filter(e => e.isDirectory());
+
+    if (dirs.length > 0 && !confirm) {
+      error(
+        `phases clear would delete ${dirs.length} phase director${dirs.length === 1 ? 'y' : 'ies'}. ` +
+        `Pass --confirm to proceed.`
+      );
+    }
+
     try {
-      const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
-      for (const entry of entries) {
-        if (!entry.isDirectory()) continue;
+      for (const entry of dirs) {
         fs.rmSync(path.join(phasesDir, entry.name), { recursive: true, force: true });
         cleared++;
       }

get-shit-done/workflows/new-milestone.md

@@ -140,7 +140,7 @@ Delete MILESTONE-CONTEXT.md if exists (consumed).
 Clear leftover phase directories from the previous milestone:
 
 ```bash
-node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" phases clear
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" phases clear --confirm
 ```
 
 ```bash