@hanzlaa/rcode 3.4.27 → 3.4.29

package/AGENTS.md

@@ -24,7 +24,7 @@ If a user says "just keep going" or "don't stop until done", that authorization
 
 - Follow [Conventional Commits](https://www.conventionalcommits.org/) format: `type(scope): subject`
 - Types allowed: `feat`, `fix`, `docs`, `style`, `refactor`, `test`, `chore`, `perf`, `revert`
-- Scopes allowed: `agents`, `skills`, `workflows`, `templates`, `dashboard`, `docs`, `config`, `github`, `commands`, `memory`, `brand`, `cli`, `ci`, `release`, `meta`, `tasks`, `migrations`, `refs`, `state`, `hooks`, `install`, `parity`, `triggers`, `dogfood`, `namespace`, `planning`, `insights`, `help`, `roadmap`, `session`, `audits`, `execute`, `executor`, `plan`, `planner`, `readme`, `sync`, `sprint`, `agent-exp`, `extensibility`, `lens-audit`, `tiers`, plus numeric phase/sprint scopes (e.g. `docs(15)`, `feat(8.3)`)
+- Scopes allowed: `agents`, `skills`, `workflows`, `templates`, `dashboard`, `docs`, `config`, `github`, `commands`, `memory`, `brand`, `cli`, `ci`, `release`, `meta`, `tasks`, `migrations`, `refs`, `state`, `hooks`, `install`, `parity`, `triggers`, `dogfood`, `namespace`, `planning`, `insights`, `help`, `roadmap`, `session`, `audits`, `execute`, `executor`, `plan`, `planner`, `readme`, `sync`, `sprint`, `agent-exp`, `extensibility`, `lens-audit`, `tiers`, `build`, `council`, `doctor`, `postinstall`, `progress`, `security`, `tools`, `uninstall`, `update`, `test`, plus numeric phase/sprint scopes (e.g. `docs(15)`, `feat(8.3)`)
 - Subject: lowercase first letter, imperative mood, no trailing period, under 72 chars
 - **NEVER add Claude/AI attribution to commit messages.** No "Generated with Claude Code", no "Co-Authored-By: Claude", no "🤖 Generated". The user does not want this.
 - **NEVER use `--no-verify`** to bypass hooks. If hooks fail, fix the underlying issue.

package/CONTRIBUTING.md

@@ -298,6 +298,16 @@ We use [Conventional Commits](https://www.conventionalcommits.org/) format. The
 - `extensibility` — extensibility and plugin hooks
 - `lens-audit` — 15-lens audit system and lenses
 - `tiers` — TIERS.md and tier-related documentation
+- `build` — `scripts/build.cjs`, esbuild config, bundle artifacts
+- `council` — `/rihal-council` workflow + spawning logic
+- `doctor` — `cli/doctor.js` health checks
+- `postinstall` — `cli/postinstall.js` lifecycle hook
+- `progress` — `/rihal-progress` workflow
+- `security` — security guardrails (symlink guards, integrity checks)
+- `test` — test files under `test/` (test-only changes)
+- `tools` — `rihal/bin/rihal-tools.cjs` subcommands
+- `uninstall` — `cli/uninstall.js` flow
+- `update` — `cli/update.js` flow
 - `<phase-id>` — numeric phase scope when committing inside a phase (e.g. `docs(15)`, `feat(8.3)`)
 - `<sprint-id>` — numeric sprint scope inside a phase (e.g. `feat(15.1)`)
 

package/cli/install.js

@@ -649,13 +649,28 @@ function seedStarterPlanning(target, projectName) {
   //   - sprint tools that previously relied on phase 01 will surface a clear
   //     "no phases yet — run /rihal-new-project first" error instead of
   //     silently operating on a fake phase
+  //
+  // Issue #705: only mark _seeded_stub when the planning ROADMAP is also
+  // a stub. If the user manually deletes state.json but has real
+  // .planning/ROADMAP.md (no INSTALL STUB banner), seeding _seeded_stub
+  // would mis-classify a real project as fresh and let /rihal-new-project
+  // overwrite it. Guard with the banner check.
   const rihalStateJson = path.join(target, '.rihal', 'state.json');
+  function planningRoadmapIsStub() {
+    const rmPath = path.join(target, '.planning', 'ROADMAP.md');
+    if (!fs.existsSync(rmPath)) return true; // missing → fresh install case
+    try {
+      const text = fs.readFileSync(rmPath, 'utf8');
+      return text.includes('<!-- INSTALL STUB');
+    } catch { return true; }
+  }
   if (!fs.existsSync(rihalStateJson)) {
     const now = new Date().toISOString();
+    const isStubProject = planningRoadmapIsStub();
     const state = {
       version: '1',
       project: null,
-      _seeded_stub: true,
+      ...(isStubProject ? { _seeded_stub: true } : {}),
       created: now,
       updated: now,
       current_phase: null,
@@ -1260,7 +1275,7 @@ function generateAgentManifest(plan, target) {
  * Generate files-manifest.csv with SHA256 per installed file. Used by
  * update/doctor to detect drift. Columns: rel, sha256, size.
  */
-function generateFilesManifest(plan, target, { mergeExistingManifest = false } = {}) {
+function generateFilesManifest(plan, target, { mergeExistingManifest = false, extraScanDirs = [] } = {}) {
   const rows = [['rel', 'sha256', 'size']];
   const newRels = new Set();
 
@@ -1273,6 +1288,34 @@ function generateFilesManifest(plan, target, { mergeExistingManifest = false } =
     newRels.add(rel);
   }
 
+  // Issue #702: skills installed via installSkills() and sidebar stubs
+  // generated by cli/generate-command-skills.cjs are NOT in the install plan
+  // (they're walked from rihal/skills/ separately and copied directly).
+  // Without this scan, files-manifest.csv was missing the largest category
+  // of installed files — orphan sweep + doctor drift detection were blind
+  // to renamed/removed skills.
+  function walkScanDir(absDir) {
+    if (!fs.existsSync(absDir)) return;
+    for (const entry of fs.readdirSync(absDir, { withFileTypes: true })) {
+      const full = path.join(absDir, entry.name);
+      if (entry.isDirectory()) {
+        walkScanDir(full);
+      } else if (entry.isFile()) {
+        const rel = path.relative(target, full).split(path.sep).join('/');
+        if (newRels.has(rel)) continue; // already in plan
+        // Skip files outside the project root (defense-in-depth — extraScanDirs
+        // is a code-controlled set, but cheap to verify).
+        if (rel.startsWith('..') || path.isAbsolute(rel)) continue;
+        try {
+          const buf = fs.readFileSync(full);
+          rows.push([rel, sha256(buf), String(buf.length)]);
+          newRels.add(rel);
+        } catch { /* unreadable file — skip */ }
+      }
+    }
+  }
+  for (const scan of extraScanDirs) walkScanDir(scan);
+
   // Merge old manifest entries that are still on disk but not in the current
   // plan — this keeps orphaned files traceable by doctor/uninstall even when
   // --force sweep was not run. Without this, a re-install without --force
@@ -1336,20 +1379,26 @@ function sweepStaleInstalledFiles(target, newPlan) {
 
   let removed = 0;
   const emptyCandidateDirs = new Set();
+  // Issue #703: a tampered or malformed CSV could contain a rel like
+  // '../../etc/passwd'. path.join collapses '..' segments and could escape
+  // the project root. Use safeRmSync's project-root containment check —
+  // any rel whose realpath escapes target is refused with reason='outside-root'.
+  const targetRoot = path.resolve(target);
   for (const rel of oldRels) {
     if (newRelsSet.has(rel)) continue;
     if (neverSweep.test(rel)) continue;
     if (isLocalOverride(rel)) continue; // #382 — never sweep user-owned overrides
+    // Reject relative paths that obviously try to escape before even hitting fs.
+    if (rel.includes('..') || path.isAbsolute(rel)) continue;
     const full = path.join(target, rel);
-    try {
-      if (fs.existsSync(full)) {
-        fs.rmSync(full, { force: true });
-        emptyCandidateDirs.add(path.dirname(full));
-        removed += 1;
-      }
-    } catch {
-      // ignore individual failures — sweep is best-effort
+    if (!fs.existsSync(full)) continue;
+    const result = safeRmSync(full, targetRoot);
+    if (result.ok) {
+      emptyCandidateDirs.add(path.dirname(full));
+      removed += 1;
     }
+    // outside-root / lstat / unlink failures are silently skipped — sweep is
+    // best-effort and we never want to abort the install on a single bad row.
   }
 
   // Remove any now-empty parent dirs (bottom-up, so nested emptiness cascades).
@@ -2073,9 +2122,28 @@ async function installInner(opts) {
     const stateSrc = path.join(SOURCE_ROOT, 'state.json');
     if (fs.existsSync(stateSrc)) {
       const now = new Date().toISOString();
-      const stateContent = fs.readFileSync(stateSrc, 'utf8')
+      let stateContent = fs.readFileSync(stateSrc, 'utf8')
         .replace(/__PROJECT_NAME__/g, opts.projectName)
         .replace(/__INSTALL_DATE__/g, now);
+
+      // Issue #705: the template ships with _seeded_stub:true. If the user
+      // already has a real planning ROADMAP (no INSTALL STUB banner) but
+      // state.json is missing (manually deleted), restoring with the stub
+      // marker would mis-classify a real project as fresh. Strip the marker
+      // when ROADMAP exists and isn't itself a stub.
+      const rmPath = path.join(opts.target, '.planning', 'ROADMAP.md');
+      if (fs.existsSync(rmPath)) {
+        try {
+          const rm = fs.readFileSync(rmPath, 'utf8');
+          if (!rm.includes('<!-- INSTALL STUB')) {
+            // Remove "_seeded_stub": true, line. JSON is small + flat enough
+            // to do this with a regex; matches whether the field is followed
+            // by a comma or sits as the last key.
+            stateContent = stateContent.replace(/^\s*"_seeded_stub":\s*true,?\s*\n/m, '');
+          }
+        } catch { /* fall through with stub marker — safe default */ }
+      }
+
       ensureDir(path.dirname(stateDest));
       writeFileAtomic(stateDest, stateContent);
     }
@@ -2101,13 +2169,12 @@ async function installInner(opts) {
   const globalAgentsDir = path.join(os.homedir(), '.rihal', 'agents');
   ensureDir(globalAgentsDir);
 
-  // files-manifest.csv — written LAST so it includes itself's siblings
-  // (but not itself, since hashing a file referencing its own hash is
-  // self-referential nonsense).
-  fs.writeFileSync(
-    path.join(configDir, 'files-manifest.csv'),
-    generateFilesManifest(plan, opts.target, { mergeExistingManifest: !opts.force }),
-  );
+  // Issue #702: files-manifest.csv used to be written here, BEFORE
+  // installSkills + generateCommandSkills ran. The 100+ skill files those
+  // functions install were therefore invisible to sweepStaleInstalledFiles
+  // and doctor's drift detection. Manifest generation moved below to AFTER
+  // all skill installations complete, with extraScanDirs covering both
+  // .claude/skills/ and .rihal/skills/ on disk.
 
   // Install v1-style phrase-activated skills (scaffold-project, create-prd,
   // retrospective, etc.) into .claude/skills/ alongside the v2 agents/commands.
@@ -2144,6 +2211,20 @@ async function installInner(opts) {
     console.log('  ' + dim(`(sidebar stub generation skipped: ${err.message})`));
   }
 
+  // Issue #702: write files-manifest.csv NOW, after all installs complete.
+  // extraScanDirs picks up the skills + sidebar stubs that aren't in the
+  // plan array.
+  fs.writeFileSync(
+    path.join(configDir, 'files-manifest.csv'),
+    generateFilesManifest(plan, opts.target, {
+      mergeExistingManifest: !opts.force,
+      extraScanDirs: [
+        path.join(opts.target, '.claude', 'skills'),
+        path.join(opts.target, '.rihal', 'skills'),
+      ],
+    }),
+  );
+
   // Seed .planning/ with starter ROADMAP + STATE so workflows work immediately
   const starterSeeded = seedStarterPlanning(opts.target, opts.projectName);
 
@@ -2167,10 +2248,14 @@ async function installInner(opts) {
     const { execFileSync } = require('child_process');
     const toolsPath = path.join(opts.target, '.rihal', 'bin', 'rihal-tools.cjs');
     if (fs.existsSync(toolsPath)) {
+      // Issue #706: 60s timeout — without it, a slow upstream URL hangs the
+      // entire install indefinitely. Brain pull is best-effort, so a timeout
+      // failure is treated identically to any other pull failure (caught below).
       const out = execFileSync('node', [toolsPath, 'brain', 'pull'], {
         cwd: opts.target,
         encoding: 'utf8',
         stdio: ['ignore', 'pipe', 'pipe'],
+        timeout: 60_000,
       });
       try { brainReport = JSON.parse(out); } catch {}
     }

package/cli/lib/manifest.cjs

@@ -109,7 +109,12 @@ function diffSet(editor, kind, expected, installed) {
  * makes doctor report drift like "agents 119/23" when nothing is wrong.
  * That's why the agent count comes from .claude/agents/, not .claude/skills/.
  */
-function verifyClaudeInstall(cwd, packageRoot) {
+function verifyClaudeInstall(cwd, packageRoot, options = {}) {
+  // Issue #698: tests assert against an isolated tempdir cwd. The global
+  // fallback (#664) makes that impossible because it reads the contributor's
+  // real ~/.claude/. Tests can pass { globalFallback: false } to disable it.
+  // Default remains true to preserve the runtime behavior introduced in #664.
+  const globalFallback = options.globalFallback !== false;
   const pkg = readPackageManifest(packageRoot);
   const agentsDir = path.join(cwd, '.claude/agents');
   const skillsDir = path.join(cwd, '.claude/skills');
@@ -129,7 +134,7 @@ function verifyClaudeInstall(cwd, packageRoot) {
   // level .claude/agents/rihal-*.md when the user's ~/.claude/ already has
   // them, to avoid duplicate commands. Without this fallback the verifier
   // reports 0 agents on every successful install in that scenario.
-  if (installedAgents.size === 0) {
+  if (installedAgents.size === 0 && globalFallback) {
     try {
       const os = require('os');
       const globalAgentsDir = path.join(os.homedir(), '.claude/agents');
@@ -143,12 +148,13 @@ function verifyClaudeInstall(cwd, packageRoot) {
     } catch { /* non-fatal — permission errors etc. */ }
   }
 
-  // Actions: .claude/skills/<bare-name>/ — exclude rihal-* dirs (those are
-  // either agent stubs or command stubs, never action skills).
+  // Actions: .claude/skills/rihal-<name>/. installSkills (cli/install.js)
+  // prefixes every action with rihal-, and readPackageManifest does the
+  // same — so both sides are normalized. The previous version filtered OUT
+  // rihal-* dirs which excluded ALL real actions and made the diff always
+  // report "everything missing." Compare directly against the prefixed set.
   const allInstalled = readInstalledDirs(skillsDir);
-  const actionsInstalled = new Set(
-    [...allInstalled].filter((n) => !n.startsWith('rihal-'))
-  );
+  const actionsInstalled = new Set([...allInstalled].filter((n) => pkg.actions.has(n)));
 
   return [
     diffSet('claude', 'agents', pkg.agents, installedAgents),

package/cli/uninstall.js

@@ -152,11 +152,22 @@ function buildPlan(cwd, editors) {
     cursor: [],
     windsurf: [],
     antigravity: [],
+    gemini: [],   // #706 — added when --editor=gemini or --editor=all
+    vscode: [],   // #706 — vscode marker dir cleanup (commands share .claude/)
     agentsMd: null, // null = no section; 'present' = section present
     stateDir: null, // null = missing; { files: N } = present
     planningDir: null, // null = missing; { files: N } = present
   };
 
+  // Issue #706: vscode and gemini are in SUPPORTED_IDES but uninstall.js had
+  // no branches for them. vscode shares .claude/ for commands+agents+skills
+  // — fold into the claude branch. gemini has its own .gemini/rihal/ tree.
+  if (editors.includes('vscode')) {
+    if (!editors.includes('claude')) editors.push('claude'); // share scan
+    const markerDir = path.join(cwd, '.vscode/rihal');
+    if (fs.existsSync(markerDir)) plan.vscode.push('.vscode/rihal');
+  }
+
   if (editors.includes('claude')) {
     const skillsDir = path.join(cwd, '.claude/skills');
     if (fs.existsSync(skillsDir)) {
@@ -212,6 +223,20 @@ function buildPlan(cwd, editors) {
     }
   }
 
+  if (editors.includes('gemini')) {
+    // #706 — gemini installs to .gemini/rihal/{agents,commands}
+    for (const sub of ['agents', 'commands']) {
+      const dir = path.join(cwd, '.gemini', 'rihal', sub);
+      if (fs.existsSync(dir)) {
+        for (const name of fs.readdirSync(dir)) {
+          if (name.startsWith('rihal-') || name.endsWith('.md')) {
+            plan.gemini.push(path.join('.gemini/rihal', sub, name));
+          }
+        }
+      }
+    }
+  }
+
   // Check AGENTS.md for Rihal section
   const agentsMdPath = path.join(cwd, 'AGENTS.md');
   if (fs.existsSync(agentsMdPath)) {
@@ -284,7 +309,23 @@ function planToPathList(plan, cwd, options = {}) {
   for (const name of plan.claude.skills) {
     paths.push(path.join('.claude/skills', name));
   }
-  if (plan.claude.commands.length > 0) {
+  // Issue #704: claude IDE installs slash commands as flat
+  // .claude/commands/rihal-*.md files (post-#697 layout). The previous
+  // backup only added the legacy '.claude/commands/rihal' subdir, so on
+  // any modern claude install the tarball was missing every slash command.
+  // Add each flat file individually if present, plus the legacy subdir.
+  for (const name of plan.claude.commands) {
+    // plan.claude.commands holds entries from BOTH layouts:
+    //   - 'rihal-foo.md' (claude flat)
+    //   - 'foo.md' (vscode subdir)
+    // Disambiguate by the rihal- prefix.
+    if (name.startsWith('rihal-') && name.endsWith('.md')) {
+      paths.push(path.join('.claude/commands', name));
+    }
+  }
+  // Legacy vscode-style subdir is added once if any subdir entries exist.
+  const hasSubdirCommand = plan.claude.commands.some(n => !n.startsWith('rihal-'));
+  if (hasSubdirCommand) {
     paths.push('.claude/commands/rihal');
   }
   for (const name of plan.claude.agents) {
@@ -299,6 +340,13 @@ function planToPathList(plan, cwd, options = {}) {
   for (const name of plan.antigravity) {
     paths.push(path.join('.antigravity/agents', name));
   }
+  // #706 — gemini paths are already relative (built that way in buildPlan).
+  if (Array.isArray(plan.gemini)) {
+    for (const rel of plan.gemini) paths.push(rel);
+  }
+  if (Array.isArray(plan.vscode)) {
+    for (const rel of plan.vscode) paths.push(rel);
+  }
   // AGENTS.md is mutated (stripped), not deleted — but we back it up so the
   // user can restore the stripped content.
   if (plan.agentsMd && fs.existsSync(path.join(cwd, 'AGENTS.md'))) {
@@ -638,6 +686,30 @@ async function runUninstall(args) {
     if (n > 0) console.log(`   ✓ removed ${n} Antigravity agents`);
   }
 
+  // #706 — gemini removal (.gemini/rihal/{agents,commands})
+  if (editors.includes('gemini')) {
+    let n = 0;
+    for (const sub of ['agents', 'commands']) {
+      const dir = path.join(cwd, '.gemini', 'rihal', sub);
+      n += removeMatching(dir, (name) => name.startsWith('rihal-') || name.endsWith('.md'));
+    }
+    removed += n;
+    if (n > 0) console.log(`   ✓ removed ${n} Gemini files`);
+  }
+
+  // #706 — vscode marker dir cleanup. Commands+skills+agents share .claude/
+  // and were already removed under the claude branch.
+  if (editors.includes('vscode')) {
+    const markerDir = path.join(cwd, '.vscode/rihal');
+    if (fs.existsSync(markerDir)) {
+      const r = safeRmSync(markerDir, path.resolve(cwd));
+      if (r.ok) {
+        removed += 1;
+        console.log(`   ✓ removed .vscode/rihal/ marker`);
+      }
+    }
+  }
+
   // Strip AGENTS.md section
   if (plan.agentsMd) {
     const agentsMdPath = path.join(cwd, 'AGENTS.md');

package/cli/update.js

@@ -33,10 +33,51 @@ const path = require('path');
 const { spawnSync } = require('child_process');
 const clack = require('@clack/prompts');
 const { PromptAbortError } = require('./lib/prompts.cjs');
-const { writeJsonAtomic } = require('./lib/fsutil.cjs');
+const { writeFileAtomic } = require('./lib/fsutil.cjs');
 const { verifyInstall, formatReport } = require('./lib/manifest.cjs');
 const install = require('./install');
 
+/**
+ * Issue #701: update.js used to read .rihal/config.json with JSON.parse, but
+ * the installer writes .rihal/config.yaml. So `rcode update` errored on
+ * every real install. Read config.yaml with the same minimal parser the
+ * installer uses, and write it back as YAML preserving every other field.
+ */
+function readConfigYaml(configPath) {
+  const text = fs.readFileSync(configPath, 'utf8');
+  const obj = {};
+  for (const raw of text.split('\n')) {
+    const line = raw.replace(/#.*$/, '').trimEnd();
+    if (!line) continue;
+    if (line.startsWith(' ')) continue; // ignore nested keys (rare; preserved on disk via raw text path)
+    const colonAt = line.indexOf(':');
+    if (colonAt === -1) continue;
+    const key = line.slice(0, colonAt).trim();
+    let val = line.slice(colonAt + 1).trim();
+    if (val.startsWith('"') && val.endsWith('"')) val = val.slice(1, -1);
+    if (val === 'true') val = true;
+    else if (val === 'false') val = false;
+    obj[key] = val;
+  }
+  return { obj, raw: text };
+}
+
+/**
+ * Surgically update a single key in a YAML config without rewriting the
+ * whole file (preserves comments, ordering, and nested keys we don't parse).
+ * If the key doesn't exist, append it.
+ */
+function setYamlKey(rawText, key, value) {
+  const re = new RegExp(`^${key}:\\s*.*$`, 'm');
+  const replacement = typeof value === 'string'
+    ? `${key}: "${value.replace(/"/g, '\\"')}"`
+    : `${key}: ${value}`;
+  if (re.test(rawText)) {
+    return rawText.replace(re, replacement);
+  }
+  return rawText.replace(/\n*$/, '') + `\n${replacement}\n`;
+}
+
 function parseArgs(args) {
   const opts = { yes: false };
   for (const arg of args) {
@@ -51,12 +92,29 @@ function parseArgs(args) {
  */
 function detectInstalledEditors(cwd) {
   const editors = [];
-  if (fs.existsSync(path.join(cwd, '.claude/skills'))) {
-    const hasRihal = fs
-      .readdirSync(path.join(cwd, '.claude/skills'))
-      .some((n) => n.startsWith('rihal-'));
-    if (hasRihal) editors.push('claude');
-  }
+
+  // Issue #701: post-#679 dedup leaves .claude/skills/ empty when ~/.claude/
+  // already has the rihal-* set. Detect "claude install" by looking at
+  // .rihal/config.yaml as the canonical signal — if config exists, the
+  // project ran rcode install at least once for claude. The presence of
+  // any commands/agents/skills then becomes secondary evidence.
+  const os = require('os');
+  const homeSkills = path.join(os.homedir(), '.claude/skills');
+  const projectClaude = (
+    (fs.existsSync(path.join(cwd, '.claude/skills')) &&
+      fs.readdirSync(path.join(cwd, '.claude/skills')).some(n => n.startsWith('rihal-'))) ||
+    (fs.existsSync(path.join(cwd, '.claude/agents')) &&
+      fs.readdirSync(path.join(cwd, '.claude/agents')).some(n => n.startsWith('rihal-'))) ||
+    (fs.existsSync(path.join(cwd, '.claude/commands')) &&
+      fs.readdirSync(path.join(cwd, '.claude/commands')).some(n => n.startsWith('rihal-')))
+  );
+  const globalClaude = (
+    fs.existsSync(homeSkills) &&
+    fs.readdirSync(homeSkills).some(n => n.startsWith('rihal-'))
+  );
+  const configIndicatesClaude = fs.existsSync(path.join(cwd, '.rihal/config.yaml'));
+  if (projectClaude || (configIndicatesClaude && globalClaude)) editors.push('claude');
+
   if (fs.existsSync(path.join(cwd, '.cursor/rules'))) {
     const hasRihal = fs
       .readdirSync(path.join(cwd, '.cursor/rules'))
@@ -241,7 +299,13 @@ async function runUpdate(args, { packageRoot, packageJson }) {
   const packageVersion = packageJson?.version || '0.0.0';
 
   // ------ Sanity: must be installed ------
-  const configPath = path.join(cwd, '.rihal/config.json');
+  // Issue #701: installer writes .rihal/config.yaml, not config.json.
+  // Tolerate both shapes for users who upgrade across the rename window,
+  // but the canonical path is YAML.
+  const configYamlPath = path.join(cwd, '.rihal/config.yaml');
+  const configJsonPath = path.join(cwd, '.rihal/config.json');
+  const configPath = fs.existsSync(configYamlPath) ? configYamlPath : configJsonPath;
+
   if (!fs.existsSync(configPath)) {
     console.error(`\n❌ Rihal Code is not installed in this directory.`);
     console.error(`   To install: rcode install\n`);
@@ -249,10 +313,18 @@ async function runUpdate(args, { packageRoot, packageJson }) {
   }
 
   let config;
+  let configRaw = '';
+  const isYaml = configPath.endsWith('.yaml');
   try {
-    config = JSON.parse(fs.readFileSync(configPath, 'utf8'));
+    if (isYaml) {
+      const parsed = readConfigYaml(configPath);
+      config = parsed.obj;
+      configRaw = parsed.raw;
+    } else {
+      config = JSON.parse(fs.readFileSync(configPath, 'utf8'));
+    }
   } catch (err) {
-    console.error(`\n❌ .rihal/config.json is not valid JSON: ${err.message}\n`);
+    console.error(`\n❌ ${path.basename(configPath)} is not parseable: ${err.message}\n`);
     process.exit(1);
   }
 
@@ -356,10 +428,18 @@ async function runUpdate(args, { packageRoot, packageJson }) {
     console.log(`   ✓ [${supportedIdes.join(', ')}] → refreshed via install.js`);
   }
 
-  // ------ Update installed_version in config.json (atomic) ------
-  config.installed_version = packageVersion;
-  writeJsonAtomic(configPath, config);
-  console.log(`   ✓ .rihal/config.json → installed_version: ${packageVersion}`);
+  // ------ Update installed_version in config (atomic) ------
+  // Issue #701: write back in the same format we read. YAML uses surgical
+  // single-key replace so other fields, comments, ordering survive.
+  if (isYaml) {
+    const updated = setYamlKey(configRaw, 'installed_version', packageVersion);
+    writeFileAtomic(configPath, updated);
+  } else {
+    config.installed_version = packageVersion;
+    const { writeJsonAtomic } = require('./lib/fsutil.cjs');
+    writeJsonAtomic(configPath, config);
+  }
+  console.log(`   ✓ ${path.relative(cwd, configPath)} → installed_version: ${packageVersion}`);
 
   // ------ Verify manifest ------
   console.log();

package/dist/rcode.js

@@ -15073,7 +15073,8 @@ var require_manifest = __commonJS({
         extra
       };
     }
-    function verifyClaudeInstall(cwd, packageRoot) {
+    function verifyClaudeInstall(cwd, packageRoot, options = {}) {
+      const globalFallback = options.globalFallback !== false;
       const pkg = readPackageManifest(packageRoot);
       const agentsDir = path2.join(cwd, ".claude/agents");
       const skillsDir = path2.join(cwd, ".claude/skills");
@@ -15085,7 +15086,7 @@ var require_manifest = __commonJS({
           }
         }
       }
-      if (installedAgents.size === 0) {
+      if (installedAgents.size === 0 && globalFallback) {
         try {
           const os = require("os");
           const globalAgentsDir = path2.join(os.homedir(), ".claude/agents");
@@ -15100,9 +15101,7 @@ var require_manifest = __commonJS({
         }
       }
       const allInstalled = readInstalledDirs(skillsDir);
-      const actionsInstalled = new Set(
-        [...allInstalled].filter((n) => !n.startsWith("rihal-"))
-      );
+      const actionsInstalled = new Set([...allInstalled].filter((n) => pkg.actions.has(n)));
       return [
         diffSet("claude", "agents", pkg.agents, installedAgents),
         diffSet("claude", "actions", pkg.actions, actionsInstalled)
@@ -15654,12 +15653,23 @@ Run \`/rihal-new-project <description>\` to bootstrap, or \`/rihal-sprint-planni
 `
       );
       const rihalStateJson = path2.join(target, ".rihal", "state.json");
+      function planningRoadmapIsStub() {
+        const rmPath = path2.join(target, ".planning", "ROADMAP.md");
+        if (!fs2.existsSync(rmPath)) return true;
+        try {
+          const text = fs2.readFileSync(rmPath, "utf8");
+          return text.includes("<!-- INSTALL STUB");
+        } catch {
+          return true;
+        }
+      }
       if (!fs2.existsSync(rihalStateJson)) {
         const now = (/* @__PURE__ */ new Date()).toISOString();
+        const isStubProject = planningRoadmapIsStub();
         const state = {
           version: "1",
           project: null,
-          _seeded_stub: true,
+          ...isStubProject ? { _seeded_stub: true } : {},
           created: now,
           updated: now,
           current_phase: null,
@@ -16103,7 +16113,7 @@ ${BLOCK}`, { mode: 493 });
       }
       return rows.map((r) => r.join(",")).join("\n") + "\n";
     }
-    function generateFilesManifest(plan, target, { mergeExistingManifest = false } = {}) {
+    function generateFilesManifest(plan, target, { mergeExistingManifest = false, extraScanDirs = [] } = {}) {
       const rows = [["rel", "sha256", "size"]];
       const newRels = /* @__PURE__ */ new Set();
       for (const entry of plan) {
@@ -16114,6 +16124,26 @@ ${BLOCK}`, { mode: 493 });
         rows.push([rel, sha256(buf), String(buf.length)]);
         newRels.add(rel);
       }
+      function walkScanDir(absDir) {
+        if (!fs2.existsSync(absDir)) return;
+        for (const entry of fs2.readdirSync(absDir, { withFileTypes: true })) {
+          const full = path2.join(absDir, entry.name);
+          if (entry.isDirectory()) {
+            walkScanDir(full);
+          } else if (entry.isFile()) {
+            const rel = path2.relative(target, full).split(path2.sep).join("/");
+            if (newRels.has(rel)) continue;
+            if (rel.startsWith("..") || path2.isAbsolute(rel)) continue;
+            try {
+              const buf = fs2.readFileSync(full);
+              rows.push([rel, sha256(buf), String(buf.length)]);
+              newRels.add(rel);
+            } catch {
+            }
+          }
+        }
+      }
+      for (const scan of extraScanDirs) walkScanDir(scan);
       if (mergeExistingManifest) {
         const manifestPath = path2.join(target, ".rihal", "_config", "files-manifest.csv");
         if (fs2.existsSync(manifestPath)) {
@@ -16149,18 +16179,18 @@ ${BLOCK}`, { mode: 493 });
       const isLocalOverride = (rel) => /\.local\.(md|mdc|json|yaml|yml|toml|js|ts)$/.test(rel);
       let removed = 0;
       const emptyCandidateDirs = /* @__PURE__ */ new Set();
+      const targetRoot = path2.resolve(target);
       for (const rel of oldRels) {
         if (newRelsSet.has(rel)) continue;
         if (neverSweep.test(rel)) continue;
         if (isLocalOverride(rel)) continue;
+        if (rel.includes("..") || path2.isAbsolute(rel)) continue;
         const full = path2.join(target, rel);
-        try {
-          if (fs2.existsSync(full)) {
-            fs2.rmSync(full, { force: true });
-            emptyCandidateDirs.add(path2.dirname(full));
-            removed += 1;
-          }
-        } catch {
+        if (!fs2.existsSync(full)) continue;
+        const result = safeRmSync(full, targetRoot);
+        if (result.ok) {
+          emptyCandidateDirs.add(path2.dirname(full));
+          removed += 1;
         }
       }
       const dirsSortedDeep = Array.from(emptyCandidateDirs).sort((a, b) => b.length - a.length);
@@ -16764,7 +16794,17 @@ commit_planning: ${desired}
         const stateSrc = path2.join(SOURCE_ROOT, "state.json");
         if (fs2.existsSync(stateSrc)) {
           const now = (/* @__PURE__ */ new Date()).toISOString();
-          const stateContent = fs2.readFileSync(stateSrc, "utf8").replace(/__PROJECT_NAME__/g, opts.projectName).replace(/__INSTALL_DATE__/g, now);
+          let stateContent = fs2.readFileSync(stateSrc, "utf8").replace(/__PROJECT_NAME__/g, opts.projectName).replace(/__INSTALL_DATE__/g, now);
+          const rmPath = path2.join(opts.target, ".planning", "ROADMAP.md");
+          if (fs2.existsSync(rmPath)) {
+            try {
+              const rm = fs2.readFileSync(rmPath, "utf8");
+              if (!rm.includes("<!-- INSTALL STUB")) {
+                stateContent = stateContent.replace(/^\s*"_seeded_stub":\s*true,?\s*\n/m, "");
+              }
+            } catch {
+            }
+          }
           ensureDir(path2.dirname(stateDest));
           writeFileAtomic(stateDest, stateContent);
         }
@@ -16782,10 +16822,6 @@ commit_planning: ${desired}
       }
       const globalAgentsDir = path2.join(os.homedir(), ".rihal", "agents");
       ensureDir(globalAgentsDir);
-      fs2.writeFileSync(
-        path2.join(configDir, "files-manifest.csv"),
-        generateFilesManifest(plan, opts.target, { mergeExistingManifest: !opts.force })
-      );
       const skillsResult = installSkills(PACKAGE_ROOT2, opts.target, {
         skipGlobalDuplicates: isProjectInstall
       });
@@ -16809,6 +16845,16 @@ commit_planning: ${desired}
       } catch (err) {
         console.log("  " + dim(`(sidebar stub generation skipped: ${err.message})`));
       }
+      fs2.writeFileSync(
+        path2.join(configDir, "files-manifest.csv"),
+        generateFilesManifest(plan, opts.target, {
+          mergeExistingManifest: !opts.force,
+          extraScanDirs: [
+            path2.join(opts.target, ".claude", "skills"),
+            path2.join(opts.target, ".rihal", "skills")
+          ]
+        })
+      );
       const starterSeeded = seedStarterPlanning(opts.target, opts.projectName);
       installBrainScaffold(PACKAGE_ROOT2, opts.target);
       const gitignoreReport = ensureRcodeGitignore(opts.target, { commitPlanning: opts.commitPlanning });
@@ -16821,7 +16867,8 @@ commit_planning: ${desired}
           const out = execFileSync("node", [toolsPath, "brain", "pull"], {
             cwd: opts.target,
             encoding: "utf8",
-            stdio: ["ignore", "pipe", "pipe"]
+            stdio: ["ignore", "pipe", "pipe"],
+            timeout: 6e4
           });
           try {
             brainReport = JSON.parse(out);
@@ -17420,9 +17467,37 @@ var require_update = __commonJS({
     var { spawnSync } = require("child_process");
     var clack = require_dist3();
     var { PromptAbortError } = require_prompts();
-    var { writeJsonAtomic } = require_fsutil();
+    var { writeFileAtomic } = require_fsutil();
     var { verifyInstall, formatReport } = require_manifest();
     var install = require_install();
+    function readConfigYaml(configPath) {
+      const text = fs2.readFileSync(configPath, "utf8");
+      const obj = {};
+      for (const raw of text.split("\n")) {
+        const line = raw.replace(/#.*$/, "").trimEnd();
+        if (!line) continue;
+        if (line.startsWith(" ")) continue;
+        const colonAt = line.indexOf(":");
+        if (colonAt === -1) continue;
+        const key = line.slice(0, colonAt).trim();
+        let val = line.slice(colonAt + 1).trim();
+        if (val.startsWith('"') && val.endsWith('"')) val = val.slice(1, -1);
+        if (val === "true") val = true;
+        else if (val === "false") val = false;
+        obj[key] = val;
+      }
+      return { obj, raw: text };
+    }
+    function setYamlKey(rawText, key, value) {
+      const re = new RegExp(`^${key}:\\s*.*$`, "m");
+      const replacement = typeof value === "string" ? `${key}: "${value.replace(/"/g, '\\"')}"` : `${key}: ${value}`;
+      if (re.test(rawText)) {
+        return rawText.replace(re, replacement);
+      }
+      return rawText.replace(/\n*$/, "") + `
+${replacement}
+`;
+    }
     function parseArgs(args) {
       const opts = { yes: false };
       for (const arg of args) {
@@ -17432,10 +17507,12 @@ var require_update = __commonJS({
     }
     function detectInstalledEditors(cwd) {
       const editors = [];
-      if (fs2.existsSync(path2.join(cwd, ".claude/skills"))) {
-        const hasRihal = fs2.readdirSync(path2.join(cwd, ".claude/skills")).some((n) => n.startsWith("rihal-"));
-        if (hasRihal) editors.push("claude");
-      }
+      const os = require("os");
+      const homeSkills = path2.join(os.homedir(), ".claude/skills");
+      const projectClaude = fs2.existsSync(path2.join(cwd, ".claude/skills")) && fs2.readdirSync(path2.join(cwd, ".claude/skills")).some((n) => n.startsWith("rihal-")) || fs2.existsSync(path2.join(cwd, ".claude/agents")) && fs2.readdirSync(path2.join(cwd, ".claude/agents")).some((n) => n.startsWith("rihal-")) || fs2.existsSync(path2.join(cwd, ".claude/commands")) && fs2.readdirSync(path2.join(cwd, ".claude/commands")).some((n) => n.startsWith("rihal-"));
+      const globalClaude = fs2.existsSync(homeSkills) && fs2.readdirSync(homeSkills).some((n) => n.startsWith("rihal-"));
+      const configIndicatesClaude = fs2.existsSync(path2.join(cwd, ".rihal/config.yaml"));
+      if (projectClaude || configIndicatesClaude && globalClaude) editors.push("claude");
       if (fs2.existsSync(path2.join(cwd, ".cursor/rules"))) {
         const hasRihal = fs2.readdirSync(path2.join(cwd, ".cursor/rules")).some((n) => n.startsWith("rihal-") && n.endsWith(".mdc"));
         if (hasRihal) editors.push("cursor");
@@ -17561,8 +17638,8 @@ var require_update = __commonJS({
       }
       if (changed) {
         content = content.replace(/\n---\n+$/, "\n");
-        const { writeFileAtomic } = require_fsutil();
-        writeFileAtomic(agentsMdPath, content);
+        const { writeFileAtomic: writeFileAtomic2 } = require_fsutil();
+        writeFileAtomic2(agentsMdPath, content);
       }
     }
     module2.exports = async function update(args, { packageRoot, packageJson }) {
@@ -17581,7 +17658,9 @@ var require_update = __commonJS({
       const cwd = process.cwd();
       const opts = parseArgs(args);
       const packageVersion = packageJson?.version || "0.0.0";
-      const configPath = path2.join(cwd, ".rihal/config.json");
+      const configYamlPath = path2.join(cwd, ".rihal/config.yaml");
+      const configJsonPath = path2.join(cwd, ".rihal/config.json");
+      const configPath = fs2.existsSync(configYamlPath) ? configYamlPath : configJsonPath;
       if (!fs2.existsSync(configPath)) {
         console.error(`
 \u274C Rihal Code is not installed in this directory.`);
@@ -17590,11 +17669,19 @@ var require_update = __commonJS({
         process.exit(1);
       }
       let config;
+      let configRaw = "";
+      const isYaml = configPath.endsWith(".yaml");
       try {
-        config = JSON.parse(fs2.readFileSync(configPath, "utf8"));
+        if (isYaml) {
+          const parsed = readConfigYaml(configPath);
+          config = parsed.obj;
+          configRaw = parsed.raw;
+        } else {
+          config = JSON.parse(fs2.readFileSync(configPath, "utf8"));
+        }
       } catch (err) {
         console.error(`
-\u274C .rihal/config.json is not valid JSON: ${err.message}
+\u274C ${path2.basename(configPath)} is not parseable: ${err.message}
 `);
         process.exit(1);
       }
@@ -17682,9 +17769,15 @@ var require_update = __commonJS({
         });
         console.log(`   \u2713 [${supportedIdes.join(", ")}] \u2192 refreshed via install.js`);
       }
-      config.installed_version = packageVersion;
-      writeJsonAtomic(configPath, config);
-      console.log(`   \u2713 .rihal/config.json \u2192 installed_version: ${packageVersion}`);
+      if (isYaml) {
+        const updated = setYamlKey(configRaw, "installed_version", packageVersion);
+        writeFileAtomic(configPath, updated);
+      } else {
+        config.installed_version = packageVersion;
+        const { writeJsonAtomic } = require_fsutil();
+        writeJsonAtomic(configPath, config);
+      }
+      console.log(`   \u2713 ${path2.relative(cwd, configPath)} \u2192 installed_version: ${packageVersion}`);
       console.log();
       const { reports, hasDrift } = verifyInstall(cwd, packageRoot, editors);
       if (hasDrift) {
@@ -17791,6 +17884,10 @@ var require_uninstall = __commonJS({
         cursor: [],
         windsurf: [],
         antigravity: [],
+        gemini: [],
+        // #706 — added when --editor=gemini or --editor=all
+        vscode: [],
+        // #706 — vscode marker dir cleanup (commands share .claude/)
         agentsMd: null,
         // null = no section; 'present' = section present
         stateDir: null,
@@ -17798,6 +17895,11 @@ var require_uninstall = __commonJS({
         planningDir: null
         // null = missing; { files: N } = present
       };
+      if (editors.includes("vscode")) {
+        if (!editors.includes("claude")) editors.push("claude");
+        const markerDir = path2.join(cwd, ".vscode/rihal");
+        if (fs2.existsSync(markerDir)) plan.vscode.push(".vscode/rihal");
+      }
       if (editors.includes("claude")) {
         const skillsDir = path2.join(cwd, ".claude/skills");
         if (fs2.existsSync(skillsDir)) {
@@ -17835,6 +17937,18 @@ var require_uninstall = __commonJS({
           plan.antigravity = fs2.readdirSync(agDir).filter((name) => name.startsWith("rihal-"));
         }
       }
+      if (editors.includes("gemini")) {
+        for (const sub of ["agents", "commands"]) {
+          const dir = path2.join(cwd, ".gemini", "rihal", sub);
+          if (fs2.existsSync(dir)) {
+            for (const name of fs2.readdirSync(dir)) {
+              if (name.startsWith("rihal-") || name.endsWith(".md")) {
+                plan.gemini.push(path2.join(".gemini/rihal", sub, name));
+              }
+            }
+          }
+        }
+      }
       const agentsMdPath = path2.join(cwd, "AGENTS.md");
       if (fs2.existsSync(agentsMdPath)) {
         const content = fs2.readFileSync(agentsMdPath, "utf8");
@@ -17881,7 +17995,13 @@ var require_uninstall = __commonJS({
       for (const name of plan.claude.skills) {
         paths.push(path2.join(".claude/skills", name));
       }
-      if (plan.claude.commands.length > 0) {
+      for (const name of plan.claude.commands) {
+        if (name.startsWith("rihal-") && name.endsWith(".md")) {
+          paths.push(path2.join(".claude/commands", name));
+        }
+      }
+      const hasSubdirCommand = plan.claude.commands.some((n) => !n.startsWith("rihal-"));
+      if (hasSubdirCommand) {
         paths.push(".claude/commands/rihal");
       }
       for (const name of plan.claude.agents) {
@@ -17896,6 +18016,12 @@ var require_uninstall = __commonJS({
       for (const name of plan.antigravity) {
         paths.push(path2.join(".antigravity/agents", name));
       }
+      if (Array.isArray(plan.gemini)) {
+        for (const rel of plan.gemini) paths.push(rel);
+      }
+      if (Array.isArray(plan.vscode)) {
+        for (const rel of plan.vscode) paths.push(rel);
+      }
       if (plan.agentsMd && fs2.existsSync(path2.join(cwd, "AGENTS.md"))) {
         paths.push("AGENTS.md");
       }
@@ -18150,6 +18276,25 @@ var require_uninstall = __commonJS({
         removed += n;
         if (n > 0) console.log(`   \u2713 removed ${n} Antigravity agents`);
       }
+      if (editors.includes("gemini")) {
+        let n = 0;
+        for (const sub of ["agents", "commands"]) {
+          const dir = path2.join(cwd, ".gemini", "rihal", sub);
+          n += removeMatching(dir, (name) => name.startsWith("rihal-") || name.endsWith(".md"));
+        }
+        removed += n;
+        if (n > 0) console.log(`   \u2713 removed ${n} Gemini files`);
+      }
+      if (editors.includes("vscode")) {
+        const markerDir = path2.join(cwd, ".vscode/rihal");
+        if (fs2.existsSync(markerDir)) {
+          const r = safeRmSync(markerDir, path2.resolve(cwd));
+          if (r.ok) {
+            removed += 1;
+            console.log(`   \u2713 removed .vscode/rihal/ marker`);
+          }
+        }
+      }
       if (plan.agentsMd) {
         const agentsMdPath = path2.join(cwd, "AGENTS.md");
         const stripped = stripRihalFromAgentsMd(agentsMdPath);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@hanzlaa/rcode",
-  "version": "3.4.27",
+  "version": "3.4.29",
   "description": "rcode — the memory bank for AI-driven SaaS teams. Persistent project context, distinctive engineering personas, and phase-based workflows. Built by Rihal. Works in Claude Code, Cursor, Gemini, VS Code, and Antigravity.",
   "main": "cli/index.js",
   "bin": {