fix(phase-3): normalize workflows and fix CLI command references

packages/cli/src/commands/config.ts

@@ -3,6 +3,8 @@
  * Extracted from cli.ts to enable modular async dispatch.
  */
 
+import * as fs from 'node:fs';
+import * as path from 'node:path';
 import { loadConfig, saveConfig, cmdOk, cmdErr } from '../core/index.js';
 import { getPositionalArg, type CommandRegistry } from './types.js';
 
@@ -61,6 +63,48 @@ export const CONFIG_COMMANDS: CommandRegistry = {
     },
   },
 
+  'config-save-defaults': {
+    name: 'config-save-defaults',
+    description: 'Save current config as a defaults snapshot. Usage: config-save-defaults <output-path>',
+    async handler(args) {
+      const dest = getPositionalArg(args, 0);
+      if (!dest) {
+        return cmdErr('Usage: config-save-defaults <output-path>');
+      }
+      const config = loadConfig(process.cwd());
+      const destPath = path.resolve(dest);
+      fs.mkdirSync(path.dirname(destPath), { recursive: true });
+      fs.writeFileSync(destPath, JSON.stringify(config, null, 2), 'utf8');
+      return cmdOk(`Defaults saved to ${destPath}`);
+    },
+  },
+
+  'validate-structure': {
+    name: 'validate-structure',
+    description: 'Validate the MaxsimCLI directory structure. Usage: validate-structure',
+    async handler(_args) {
+      const projectDir = process.cwd();
+      const checks = [
+        { path: '.claude', label: '.claude/ directory' },
+        { path: path.join('.claude', 'maxsim'), label: '.claude/maxsim/ directory' },
+        { path: path.join('.claude', 'maxsim', 'bin', 'maxsim-tools.cjs'), label: '.claude/maxsim/bin/maxsim-tools.cjs' },
+        { path: path.join('.claude', 'maxsim', 'config.json'), label: '.claude/maxsim/config.json' },
+      ];
+
+      const results: string[] = [];
+      let allPassed = true;
+      for (const check of checks) {
+        const fullPath = path.join(projectDir, check.path);
+        const exists = fs.existsSync(fullPath);
+        results.push(`${exists ? 'PASS' : 'FAIL'}: ${check.label}`);
+        if (!exists) allPassed = false;
+      }
+
+      const summary = allPassed ? 'All checks passed.' : 'Some checks failed.';
+      return cmdOk(`${results.join('\n')}\n${summary}`);
+    },
+  },
+
   'config-ensure-section': {
     name: 'config-ensure-section',
     description: 'Create a top-level config section if it does not already exist.',

packages/cli/src/commands/github.ts

@@ -386,7 +386,7 @@ export const GITHUB_COMMANDS: CommandRegistry = {
 
   'post-comment': {
     name: 'post-comment',
-    description: 'Post a comment on an issue. Usage: post-comment --issue-number 216 --body "text" [--body-file /path] [--type plan]',
+    description: 'Post a comment on an issue. Usage: post-comment --issue-number 216 --body "text" [--body-file /path] [--type plan] [--plan-number 1]',
     async handler(args) {
       let issueNumber: number;
       try {
@@ -413,8 +413,13 @@ export const GITHUB_COMMANDS: CommandRegistry = {
       }
 
       const commentType = getFlag(args, '--type');
+      const planNumber = getIntFlag(args, '--plan-number');
       if (commentType) {
-        const header = formatCommentHeader({ type: commentType as Parameters<typeof formatCommentHeader>[0]['type'] });
+        const meta: Record<string, unknown> = { type: commentType };
+        if (planNumber !== undefined && !Number.isNaN(planNumber)) {
+          meta.plan = planNumber;
+        }
+        const header = formatCommentHeader(meta as Parameters<typeof formatCommentHeader>[0]);
         body = `${header}\n${body}`;
       }
 
@@ -573,7 +578,7 @@ export const GITHUB_COMMANDS: CommandRegistry = {
 
   'delete-comments': {
     name: 'delete-comments',
-    description: 'Delete comments of a given type from an issue. Usage: delete-comments --issue-number 216 --type plan',
+    description: 'Delete comments of a given type from an issue. Supports comma-separated types. Usage: delete-comments --issue-number 216 --type plan,context,research',
     async handler(args) {
       let issueNumber: number;
       try {
@@ -584,26 +589,30 @@ export const GITHUB_COMMANDS: CommandRegistry = {
         return cmdErr((e as Error).message);
       }
 
-      let type: string;
+      let typeRaw: string;
       try {
-        type = getRequiredFlag(args, '--type');
+        typeRaw = getRequiredFlag(args, '--type');
       } catch (e) {
         return cmdErr((e as Error).message);
       }
 
+      // Support comma-separated types (e.g. "plan,context,research")
+      const types = new Set(typeRaw.split(',').map((t) => t.trim()).filter(Boolean));
+
       const commentsResult = await listComments(issueNumber);
       if (!commentsResult.ok) return cmdErr(commentsResult.error);
 
-      const matching = commentsResult.data.filter(
-        (c) => parseCommentMeta(c.body)?.type === type,
-      );
+      const matching = commentsResult.data.filter((c) => {
+        const meta = parseCommentMeta(c.body);
+        return meta ? types.has(meta.type) : false;
+      });
 
       for (const comment of matching) {
         const deleteResult = await deleteComment(comment.id);
         if (!deleteResult.ok) return cmdErr(deleteResult.error);
       }
 
-      return cmdOk(`Deleted ${matching.length} ${type} comments from #${issueNumber}`);
+      return cmdOk(`Deleted ${matching.length} [${[...types].join(',')}] comments from #${issueNumber}`);
     },
   },
 
@@ -684,15 +693,6 @@ export const GITHUB_COMMANDS: CommandRegistry = {
     },
   },
 
-  'set-status': {
-    name: 'set-status',
-    description: 'Set an issue status on the project board (alias for move-issue). Usage: set-status --issue-number 216 --status "Done"',
-    async handler(args) {
-      // Delegate to move-issue handler
-      return GITHUB_COMMANDS['move-issue'].handler(args);
-    },
-  },
-
   // ── Task 3.1: GitHub status diagnostic ──────────────────────────────
 
   'status': {
@@ -1041,13 +1041,13 @@ export const GITHUB_COMMANDS: CommandRegistry = {
     name: 'all-progress',
     description: 'Show adaptive progress for all phase issues with detail levels and progress bar. Usage: all-progress',
     async handler(_args) {
-      // Fetch all phase issues (label is 'maxsim:phase' per actual GitHub data)
-      const result = await listIssues({ labels: 'maxsim:phase', state: 'all' });
+      // Fetch all phase issues by canonical label (type:phase per types.ts)
+      const result = await listIssues({ labels: 'type:phase', state: 'all' });
       if (!result.ok) return cmdErr(result.error);
 
       const phases = result.data;
       if (phases.length === 0) {
-        return cmdOk('No phase issues found (label: maxsim:phase)');
+        return cmdOk('No phase issues found (label: type:phase)');
       }
 
       // Extract phase number from title (e.g., "Phase 2: ..." → 2) for sorting