cohorte 1.6.0 → 2.0.0

package/dashboard/server/doctor.js

@@ -1,5 +1,5 @@
 'use strict';
-// Programmatic port of the /doctor checks (core/commands/doctor.md), for the dashboard.
+// Programmatic port of the /cohorte-doctor checks (core/commands/doctor.md), for the dashboard.
 // Read-only: inspects files only. Checks that need a live process (MCP connectivity,
 // git worktree state, DesignSync) are reported as `skip` with a note — the node server
 // can't run them, and honest "not checked here" beats a false green.
@@ -20,14 +20,14 @@ const FIXED_AGENTS = new Set([
 ]);
 
 // The spec lifecycle (SCHEMA.md §Spec status). `in-progress` and `blocked` are written by
-// the /drive driver — they are what makes an interrupted autonomous loop resumable, so a
+// the /cohorte-loop driver — they are what makes an interrupted autonomous loop resumable, so a
 // dashboard that flagged them as invalid would report the pipeline's own state as a defect.
 const VALID_STATUS = ['draft', 'frozen', 'in-progress', 'in-review', 'shipped', 'blocked'];
 
 // Artifacts the pipeline itself writes into specs/ that are NOT feature specs and have no
-// front-matter status. `/audit` writes specs/refactor-backlog.md by design, so scanning it
-// as a spec made /doctor warn about a file cohorte had just created — a false positive that
-// fired in every project that had ever run /audit. `_`-prefixed files (e.g. _template.md)
+// front-matter status. `/cohorte-audit` writes specs/refactor-backlog.md by design, so scanning it
+// as a spec made /cohorte-doctor warn about a file cohorte had just created — a false positive that
+// fired in every project that had ever run /cohorte-audit. `_`-prefixed files (e.g. _template.md)
 // are already skipped by the reader below.
 const NON_SPEC_FILES = new Set(['refactor-backlog.md']);
 
@@ -62,7 +62,7 @@ function checkCore(v) {
   if (v.freshness === -1) {
     return mk('core', 'Core & pointer', 'warn',
       `core ${v.installedVersion} installed (${v.installMode}); npm latest is ${v.latest}`,
-      '/update-pipeline   (or  npx cohorte update)');
+      '/cohorte-update-pipeline   (or  npx cohorte update)');
   }
   const tail = v.latest ? `, npm latest ${v.latest}` : ', npm unreachable';
   return mk('core', 'Core & pointer', 'ok', `core ${v.installedVersion} (${v.installMode})${tail}`);
@@ -71,12 +71,12 @@ function checkCore(v) {
 function checkProfile(profile, hasPipelineMd) {
   if (!hasPipelineMd) {
     return mk('profile', 'Profile (PIPELINE.md)', 'bad', 'PIPELINE.md not found',
-      '/init-pipeline   (generate the project profile)');
+      '/cohorte-init-pipeline   (generate the project profile)');
   }
   if (!profile) {
     return mk('profile', 'Profile (PIPELINE.md)', 'bad',
       'PIPELINE.md present but its `yaml pipeline-profile` block is missing or unparseable',
-      '/init-pipeline   (or fix the fenced yaml block)');
+      '/cohorte-init-pipeline   (or fix the fenced yaml block)');
   }
   const n = (profile.surfaces || []).length;
   return mk('profile', 'Profile (PIPELINE.md)', n ? 'ok' : 'warn',
@@ -101,7 +101,7 @@ function checkAgents(profile, projectRoot) {
   if (missing.length) {
     return mk('agents', 'Surfaces ↔ agents', 'bad',
       `surface(s) with no rendered agent: ${missing.join(', ')}`,
-      '/init-pipeline   (re-render surface agents)');
+      '/cohorte-init-pipeline   (re-render surface agents)');
   }
   if (orphans.length) {
     return mk('agents', 'Surfaces ↔ agents', 'warn',
@@ -120,7 +120,7 @@ function checkGate(profile, projectRoot) {
   const cfg = readJson(path.join(projectRoot, '.claude', 'gate-config.json'));
   if (!cfg) {
     return mk('gate', 'Gate config', 'bad', '.claude/gate-config.json missing or unreadable',
-      '/init-pipeline   (regenerate gate-config.json from the gate block)');
+      '/cohorte-init-pipeline   (regenerate gate-config.json from the gate block)');
   }
   const drifted = [];
   if (!sameSet(cfg.deny, gate.deny)) drifted.push('deny');
@@ -147,6 +147,55 @@ function checkGate(profile, projectRoot) {
     (branchGated ? `, ${branchGated} gated on ${gate.default_branch || 'main'}` : '') + ')');
 }
 
+// Local-only pipeline artifacts. `.claude/preflight.ok` is the one that BREAKS things when
+// versioned rather than merely being noise: the stamp names the tree it verified, committing
+// it moves HEAD past that, and the committed copy then rides into every fresh clone and
+// worktree — the phase gate either blocks a clean tree or greens one it never checked.
+const LOCAL_ARTIFACTS = [
+  { path: '.claude/preflight.ok', why: 'the phase-gate stamp — a versioned one breaks the gate in every clone and worktree' },
+  { path: '.claude/pipeline-metrics.jsonl', why: 'the per-dispatch metrics sink (local, append-only)' },
+  { path: 'specs/reports/', why: 'the /cohorte-review report buffer (derived, regenerated each run)' },
+];
+
+// Does any .gitignore in play cover `rel`? Deliberately literal — it recognizes the exact
+// path, its basename, a trailing-slash dir prefix and a `*.<ext>` glob, which is every form
+// /cohorte-init-pipeline writes. Anything more clever would need a real gitignore engine.
+function ignoreCovers(projectRoot, rel) {
+  const base = rel.replace(/\/$/, '').split('/').pop();
+  const ext = base.includes('.') ? '*' + base.slice(base.lastIndexOf('.')) : null;
+  const files = [
+    path.join(projectRoot, '.gitignore'),
+    path.join(projectRoot, '.claude', '.gitignore'),
+  ];
+  for (const f of files) {
+    const text = readText(f);
+    if (!text) continue;
+    for (let line of text.split('\n')) {
+      line = line.trim();
+      if (!line || line.startsWith('#')) continue;
+      const p = line.replace(/^\/+/, '').replace(/\/+$/, '');
+      if (!p) continue;
+      if (p === rel.replace(/\/$/, '') || p === base || p === ext) return true;
+      // A directory rule covers everything under it (`.claude/` ignores the stamp too).
+      if (rel.startsWith(p + '/')) return true;
+    }
+  }
+  return false;
+}
+
+function checkLocalArtifacts(projectRoot) {
+  const unignored = LOCAL_ARTIFACTS.filter(a => !ignoreCovers(projectRoot, a.path));
+  if (!unignored.length) {
+    return mk('artifacts', 'Local artifacts', 'ok',
+      `${LOCAL_ARTIFACTS.length} local-only artifact path(s) all gitignored`);
+  }
+  const stamp = unignored.find(a => a.path === '.claude/preflight.ok');
+  return mk('artifacts', 'Local artifacts', stamp ? 'bad' : 'warn',
+    `not gitignored: ${unignored.map(a => a.path).join(', ')} — ${unignored[0].why}`,
+    `add ${unignored.map(a => a.path).join(' + ')} to .gitignore`
+    + (stamp ? ', then `git rm --cached --ignore-unmatch .claude/preflight.ok`' : ''));
+}
+
 function gateRegs(settingsPath) {
   const data = readJson(settingsPath);
   const pre = data && data.hooks && Array.isArray(data.hooks.PreToolUse) ? data.hooks.PreToolUse : [];
@@ -159,7 +208,7 @@ function gateRegs(settingsPath) {
 
 function checkHooks(projectRoot, globalDir, installMode) {
   // A registration in EITHER scope serves the project: bundled repos get it from
-  // /init-pipeline in project settings, but on a machine with the global core the
+  // /cohorte-init-pipeline in project settings, but on a machine with the global core the
   // hook usually lives (correctly, exactly once) in global settings — warning
   // there would prescribe a re-registration that double-prompts.
   const scopes = [
@@ -173,7 +222,7 @@ function checkHooks(projectRoot, globalDir, installMode) {
     return mk('hooks', 'Gate hook', 'warn', 'gate.py not registered in project or global settings.json',
       installMode === 'global'
         ? 'npx cohorte install --global   (re-registers the hook)'
-        : '/init-pipeline   (register the PreToolUse gate hook)');
+        : '/cohorte-init-pipeline   (register the PreToolUse gate hook)');
   }
   const total = found.reduce((n, s) => n + s.regs.length, 0);
   if (total > 1) {
@@ -195,7 +244,7 @@ function checkRetrieval(profile, projectRoot) {
   if (!provider || provider === 'none' || String(provider).startsWith('<')) {
     return mk('retrieval', 'Code retrieval', 'skip', 'provider: none');
   }
-  // The profile alone isn't proof the provider was ever wired: /init-pipeline
+  // The profile alone isn't proof the provider was ever wired: /cohorte-init-pipeline
   // registers it at project scope in .mcp.json. Verify the entry exists on disk;
   // live connectivity still needs a session — note it, don't fake green.
   const mcp = readJson(path.join(projectRoot, '.mcp.json'));
@@ -204,10 +253,10 @@ function checkRetrieval(profile, projectRoot) {
   if (!wired) {
     return mk('retrieval', 'Code retrieval', 'warn',
       `profile says provider: ${provider} but .mcp.json has no matching server entry`,
-      '/init-pipeline or /update-pipeline   (re-wire the retrieval provider)');
+      '/cohorte-init-pipeline or /cohorte-update-pipeline   (re-wire the retrieval provider)');
   }
   return mk('retrieval', 'Code retrieval', 'ok',
-    `provider: ${provider} — registered in .mcp.json (connectivity needs /doctor in-session)`);
+    `provider: ${provider} — registered in .mcp.json (connectivity needs /cohorte-doctor in-session)`);
 }
 
 function checkDesign(profile, projectRoot) {
@@ -234,14 +283,14 @@ function checkIsolation(profile, projectRoot) {
   }
   if (problems.length) {
     return mk('isolation', 'Isolation', 'warn', problems.join('; '),
-      '/init-pipeline   (re-render the isolation scripts)');
+      '/cohorte-init-pipeline   (re-render the isolation scripts)');
   }
   return mk('isolation', 'Isolation', 'ok', 'feature scripts rendered (worktree state not checked here)');
 }
 
 // Workflow variants (review/audit/refactor as deterministic multi-agent runs) are opt-in;
 // the conversational commands stay the default path, so nothing here is ever 'bad'.
-// Whether the session has workflows ENABLED needs a live Claude session — /doctor
+// Whether the session has workflows ENABLED needs a live Claude session — /cohorte-doctor
 // in-session checks that; here we only check what's on disk.
 function checkWorkflows(projectRoot, globalDir, installMode) {
   if (installMode === 'none') return mk('workflows', 'Workflows', 'skip', 'no core installed');
@@ -269,7 +318,7 @@ function checkWorkflows(projectRoot, globalDir, installMode) {
   }
   return mk('workflows', 'Workflows', 'ok',
     'scripts + profile-reader installed — opt-in per run; needs Claude Code ≥ 2.1.154 with ' +
-    'workflows enabled (run /doctor in-session to check the live half)');
+    'workflows enabled (run /cohorte-doctor in-session to check the live half)');
 }
 
 function scanSpecs(projectRoot) {
@@ -284,7 +333,7 @@ function scanSpecs(projectRoot) {
     const body = fm ? fm[1] : '';
     const get = k => { const m = body.match(new RegExp(`^${k}:\\s*(.*)$`, 'm')); return m ? m[1].trim() : null; };
     const status = get('status');
-    // The loop driver's resume state, when a /drive is (or was) running on this spec.
+    // The loop driver's resume state, when a /cohorte-loop is (or was) running on this spec.
     const pass = parseInt(get('loop_pass'), 10);
     const phase = get('loop_phase');
     specs.push({
@@ -327,6 +376,7 @@ async function state({ projectRoot, globalDir, cliVersion }) {
     checkProfile(profile, pipelineMd != null),
     checkAgents(profile, projectRoot),
     checkGate(profile, projectRoot),
+    checkLocalArtifacts(projectRoot),
     checkHooks(projectRoot, globalDir, v.installMode),
     checkRetrieval(profile, projectRoot),
     checkDesign(profile, projectRoot),

package/dashboard/server/index.js

@@ -143,8 +143,8 @@ function runAction(req, res, body, { pkgRoot }) {
 function runClaude(req, res, body) {
   const project = body.project ? path.resolve(body.project) : null;
   const command = String(body.command || '');
-  if (!/^\/(init-pipeline|update-pipeline|audit)$/.test(command)) {
-    return sendJson(res, 400, { error: 'unsupported command (only /init-pipeline, /update-pipeline or /audit)' });
+  if (!/^\/cohorte-(init-pipeline|update-pipeline|audit)$/.test(command)) {
+    return sendJson(res, 400, { error: 'unsupported command (only /cohorte-init-pipeline, /cohorte-update-pipeline or /cohorte-audit)' });
   }
   if (!project || !fs.existsSync(project)) {
     return sendJson(res, 400, { error: 'project path not found' });
@@ -174,7 +174,7 @@ function runClaude(req, res, body) {
 // Full project reset: back up the project's pipeline footprint (.claude/, PIPELINE.md, and
 // optionally specs/) to .claude.bak-<ts>, remove it, then reinstall a fresh BUNDLED core (or,
 // for global-mode projects, leave the shared ~/.claude core untouched). Never touches ~/.claude.
-// Streams progress; ends with __EXIT__ <code>. The profile is regenerated by /init-pipeline after.
+// Streams progress; ends with __EXIT__ <code>. The profile is regenerated by /cohorte-init-pipeline after.
 function runReset(req, res, body, { pkgRoot, globalDir }) {
   const project = body.project ? path.resolve(body.project) : null;
   const purgeSpecs = !!body.purgeSpecs;
@@ -230,14 +230,14 @@ function runReset(req, res, body, { pkgRoot, globalDir }) {
       child.stdout.on('data', d => res.write(d));
       child.stderr.on('data', d => res.write(d));
       child.on('close', code => {
-        log('\n✔ Reset complete. Now run  /init-pipeline  in Claude Code to regenerate PIPELINE.md + the surface agents.');
+        log('\n✔ Reset complete. Now run  /cohorte-init-pipeline  in Claude Code to regenerate PIPELINE.md + the surface agents.');
         done(code);
       });
       child.on('error', err => { log(`\nspawn error: ${err.message}`); done(1); });
       req.on('close', () => { try { child.kill(); } catch { /* already gone */ } });
     } else {
       log('\n✔ Reset complete. The shared global core stays installed in ~/.claude.');
-      log('Now run  /init-pipeline  in Claude Code to regenerate this project\'s PIPELINE.md + agents.');
+      log('Now run  /cohorte-init-pipeline  in Claude Code to regenerate this project\'s PIPELINE.md + agents.');
       done(0);
     }
   } catch (e) {

package/dashboard/server/metrics.js

@@ -1,6 +1,6 @@
 'use strict';
 // Read a project's `.claude/pipeline-metrics.jsonl` (one line per phase batch, appended by
-// /build, /review and /fix) and aggregate it per feature: wall-clock per phase, fix
+// /cohorte-build, /cohorte-review and /cohorte-fix) and aggregate it per feature: wall-clock per phase, fix
 // rounds, and per-surface results. Dependency-free; a missing file is simply "no data yet".
 //
 // Two line formats coexist in the file:

package/install.ps1

@@ -14,7 +14,7 @@
 #     .\install.ps1 -Update -Global
 #
 # Per-project install copies the core into <target>\.claude; global install copies it once
-# into ~\.claude and registers the gate hook there. Either way you then run `/init-pipeline`
+# into ~\.claude and registers the gate hook there. Either way you then run `/cohorte-init-pipeline`
 # in each repo to generate PIPELINE.md + render the surface agents. Update refreshes ONLY the
 # stack-agnostic files; generated profiles, rendered agents, gate-config.json and any project
 # settings.json are left untouched.
@@ -152,6 +152,7 @@ try {
         Copy-Item (Join-Path $src 'scripts\telemetry-send.sh')    (Join-Path $dest 'pipeline\scripts') -Force
         Copy-Item (Join-Path $src 'scripts\preflight.sh')         (Join-Path $dest 'pipeline\scripts') -Force
         Copy-Item (Join-Path $src 'scripts\loop.sh')              (Join-Path $dest 'pipeline\scripts') -Force
+        Copy-Item (Join-Path $src 'scripts\loop-detach.sh')       (Join-Path $dest 'pipeline\scripts') -Force
         Copy-Item (Join-Path $src 'core\agents\implementer.template.md') (Join-Path $dest 'pipeline') -Force
         if (Test-Path (Join-Path $src 'CHANGELOG.md')) { Copy-Item (Join-Path $src 'CHANGELOG.md') (Join-Path $dest 'pipeline') -Force }
         [System.IO.File]::WriteAllText((Join-Path $dest 'pipeline\VERSION'), "$ver`n", [System.Text.UTF8Encoding]::new($false))
@@ -201,6 +202,14 @@ try {
         # 1.6.0 renamed /loop → /drive: Claude Code's own built-in /loop shadowed ours, so a leftover
         # commands\loop.md is a command the user can never reach — scrub it rather than leave a decoy.
         Remove-Item -LiteralPath (Join-Path $dest 'commands\loop.md') -Force -ErrorAction SilentlyContinue
+        # 2.0.0 prefixed every command with `cohorte-`, which ends the shadowing problem for good.
+        # Copy-Item never deletes, so all 13 bare names would survive an upgrade as decoys — and a
+        # stale /build is the worst kind: it still dispatches implementers, from a 1.x command file
+        # that knows nothing of this core's contract. /drive goes too (it became /cohorte-loop).
+        foreach ($c in @('align-ds','audit','brainstorm','build','doctor','drive','fix',
+                         'init-pipeline','refactor','review','ship','spec','update-pipeline')) {
+            Remove-Item -LiteralPath (Join-Path $dest "commands\$c.md") -Force -ErrorAction SilentlyContinue
+        }
         # 0.1.19 split the bi-mode questionnaire-researcher into research-agent + questionnaire-architect;
         # copy-over never deletes, so scrub the retired agent lest a dead subagent_type linger.
         Remove-Item -LiteralPath (Join-Path $dest 'agents\questionnaire-researcher.md') -Force -ErrorAction SilentlyContinue
@@ -224,8 +233,8 @@ try {
 
     # pipeline capability config is USER-level (vault, Notion DB, kanban boards) — it lives in
     # the user's .claude regardless of install scope. Seed only if neither the consolidated nor
-    # the legacy copy exists. Non-interactive here: seeds disabled defaults; /init-pipeline +
-    # /update-pipeline wire it (npx's installer offers a quick interview instead).
+    # the legacy copy exists. Non-interactive here: seeds disabled defaults; /cohorte-init-pipeline +
+    # /cohorte-update-pipeline wire it (npx's installer offers a quick interview instead).
     function Initialize-Config {
         $userClaude = if ($env:CLAUDE_CONFIG_DIR) { $env:CLAUDE_CONFIG_DIR } else { Join-Path $HOME '.claude' }
         $cfg = Join-Path $userClaude 'cohorte.config.yaml'
@@ -237,11 +246,11 @@ try {
             Write-Host "  - kept your existing $cfg"
         } elseif ($legacy) {
             Write-Host "  - found legacy $legacy — kept as-is (read as a fallback)."
-            Write-Host "    Run /update-pipeline to migrate it into cohorte.config.yaml + wire the kanban."
+            Write-Host "    Run /cohorte-update-pipeline to migrate it into cohorte.config.yaml + wire the kanban."
         } else {
             New-Item -ItemType Directory -Force -Path $userClaude | Out-Null
             Copy-Item (Join-Path $src 'profile\cohorte.config.template.yaml') $cfg
-            Write-Host "  - seeded $cfg (disabled defaults — enable via /init-pipeline or /update-pipeline)"
+            Write-Host "  - seeded $cfg (disabled defaults — enable via /cohorte-init-pipeline or /cohorte-update-pipeline)"
         }
     }
 
@@ -318,24 +327,24 @@ try {
 OK pipeline core installed globally into $dest  (version $ver)
   gate hook: $hookState  (reads each repo's .claude/gate-config.json; silent where absent)
 
-The commands (/init-pipeline, /brainstorm, /build ...) and the review/release agents are now
+The commands (/cohorte-init-pipeline, /cohorte-brainstorm, /cohorte-build ...) and the review/release agents are now
 available in EVERY project on this machine — nothing is copied per repo.
 
 Per repo:
   1. Open the project in Claude Code.
-  2. Run  /init-pipeline  — it generates PIPELINE.md, renders the surface agents, writes
+  2. Run  /cohorte-init-pipeline  — it generates PIPELINE.md, renders the surface agents, writes
      .claude/gate-config.json, and drops a committed .claude/pipeline.json pointer so
      teammates know to install the global core ($repoUrl).
-  3. Commit PIPELINE.md + .claude/, then  /brainstorm  to start a feature.
+  3. Commit PIPELINE.md + .claude/, then  /cohorte-brainstorm  to start a feature.
 
-Code retrieval (Serena — the default provider /init-pipeline wires per repo):
+Code retrieval (Serena — the default provider /cohorte-init-pipeline wires per repo):
   uv tool install -p 3.13 serena-agent   # once per machine
   Make sure the uv tools dir is on PATH (uv tool update-shell) — otherwise the
   registered MCP server silently fails to start.
 
 Global kanban config, user-scoped — optional:
   · One consolidated file: ~/.claude/cohorte.config.yaml (don't hand-edit it).
-  · /init-pipeline (new project) and /update-pipeline (existing) wire it for you: creating +
+  · /cohorte-init-pipeline (new project) and /cohorte-update-pipeline (existing) wire it for you: creating +
     syncing an Obsidian kanban board of the pipeline in your shared vault.
 "@
         return
@@ -356,11 +365,11 @@ OK pipeline core installed into $dest  (version $ver)
 
 Next:
   1. Open the project in Claude Code.
-  2. Run  /init-pipeline   — it detects your stack, asks the gaps, and generates
+  2. Run  /cohorte-init-pipeline   — it detects your stack, asks the gaps, and generates
      PIPELINE.md + renders one implementer agent per surface.
-  3. Commit PIPELINE.md, then  /brainstorm  to start a feature.
+  3. Commit PIPELINE.md, then  /cohorte-brainstorm  to start a feature.
 
-Code retrieval (Serena — the default provider /init-pipeline wires per repo):
+Code retrieval (Serena — the default provider /cohorte-init-pipeline wires per repo):
   uv tool install -p 3.13 serena-agent   # once per machine
   Make sure the uv tools dir is on PATH (uv tool update-shell) — otherwise the
   registered MCP server silently fails to start.
@@ -378,7 +387,7 @@ Prefer one shared core across all your repos?  Re-run with  -Global.
         Write-Host @"
 
 OK core refreshed to $ver. Your PIPELINE.md, rendered surface agents, gate-config.json and
-  settings.json were left as-is. Re-run /init-pipeline if your stack changed.
+  settings.json were left as-is. Re-run /cohorte-init-pipeline if your stack changed.
 "@
     }
 } finally {

package/install.sh

@@ -16,7 +16,7 @@
 #     sh install.sh --update --global
 #
 # Per-project install copies the core into <target>/.claude; global install copies it once
-# into ~/.claude and registers the gate hook there. Either way you then run `/init-pipeline`
+# into ~/.claude and registers the gate hook there. Either way you then run `/cohorte-init-pipeline`
 # in each repo to generate PIPELINE.md + render the surface agents. Update refreshes ONLY the
 # stack-agnostic files; generated profiles, rendered agents, gate-config.json and any project
 # settings.json are left untouched.
@@ -108,8 +108,10 @@ copy_core() {
   cp "$src/scripts/telemetry-send.sh"    "$dest/pipeline/scripts/"
   cp "$src/scripts/preflight.sh"         "$dest/pipeline/scripts/"
   cp "$src/scripts/loop.sh"              "$dest/pipeline/scripts/"
+  cp "$src/scripts/loop-detach.sh"       "$dest/pipeline/scripts/"
   chmod +x "$dest/pipeline/scripts/kanban-move.sh" "$dest/pipeline/scripts/telemetry-send.sh" \
-           "$dest/pipeline/scripts/preflight.sh" "$dest/pipeline/scripts/loop.sh" 2>/dev/null || true
+           "$dest/pipeline/scripts/preflight.sh" "$dest/pipeline/scripts/loop.sh" \
+           "$dest/pipeline/scripts/loop-detach.sh" 2>/dev/null || true
   cp "$src/core/agents/implementer.template.md" "$dest/pipeline/"
   [ -f "$src/CHANGELOG.md" ] && cp "$src/CHANGELOG.md" "$dest/pipeline/"
   printf '%s\n' "$ver" > "$dest/pipeline/VERSION"
@@ -161,6 +163,14 @@ copy_fixed_agents() {
   # 1.6.0 renamed /loop → /drive: Claude Code's own built-in /loop shadowed ours, so a leftover
   # commands/loop.md is a command the user can never reach — scrub it rather than leave a decoy.
   rm -f "$dest/commands/loop.md"
+  # 2.0.0 prefixed every command with `cohorte-`, which ends the shadowing problem for good.
+  # Copy-over never deletes, so all 13 bare names would survive an upgrade as decoys — and a
+  # stale /build is the worst kind: it still dispatches implementers, from a 1.x command file
+  # that knows nothing of this core's contract. /drive goes too (it became /cohorte-loop).
+  for c in align-ds audit brainstorm build doctor drive fix init-pipeline \
+           refactor review ship spec update-pipeline; do
+    rm -f "$dest/commands/$c.md"
+  done
   # 0.1.19 split the bi-mode questionnaire-researcher into research-agent + questionnaire-architect;
   # copy-over never deletes, so scrub the retired agent lest a dead subagent_type linger.
   rm -f "$dest/agents/questionnaire-researcher.md"
@@ -186,7 +196,7 @@ scrub_research_questionnaire() {
 # pipeline capability config is USER-level (vault, Notion DB, kanban boards) — it lives in
 # ~/.claude regardless of install scope. Seed it only if neither the consolidated nor the
 # legacy copy exists. This piped installer is non-interactive: it seeds disabled defaults;
-# /init-pipeline + /update-pipeline wire it (npx's installer offers a quick interview instead).
+# /cohorte-init-pipeline + /cohorte-update-pipeline wire it (npx's installer offers a quick interview instead).
 seed_config() {
   base="${CLAUDE_CONFIG_DIR:-$HOME/.claude}"
   cfg="$base/cohorte.config.yaml"
@@ -198,11 +208,11 @@ seed_config() {
     echo "  · kept your existing $cfg"
   elif [ -n "$legacy" ]; then
     echo "  · found legacy $legacy — kept as-is (read as a fallback)."
-    echo "    Run /update-pipeline to migrate it into cohorte.config.yaml + wire the kanban."
+    echo "    Run /cohorte-update-pipeline to migrate it into cohorte.config.yaml + wire the kanban."
   else
     mkdir -p "$base"
     cp "$src/profile/cohorte.config.template.yaml" "$cfg"
-    echo "  · seeded $cfg (disabled defaults — enable via /init-pipeline or /update-pipeline)"
+    echo "  · seeded $cfg (disabled defaults — enable via /cohorte-init-pipeline or /cohorte-update-pipeline)"
   fi
 }
 
@@ -290,24 +300,24 @@ if [ "$scope" = "global" ]; then
 ✓ pipeline core installed globally into $dest  (version $ver)
   gate hook: $hook_state  (reads each repo's .claude/gate-config.json; silent where absent)
 
-The commands (/init-pipeline, /brainstorm, /build …) and the review/release agents are now
+The commands (/cohorte-init-pipeline, /cohorte-brainstorm, /cohorte-build …) and the review/release agents are now
 available in EVERY project on this machine — nothing is copied per repo.
 
 Per repo:
   1. Open the project in Claude Code.
-  2. Run  /init-pipeline  — it generates PIPELINE.md, renders the surface agents, writes
+  2. Run  /cohorte-init-pipeline  — it generates PIPELINE.md, renders the surface agents, writes
      .claude/gate-config.json, and drops a committed .claude/pipeline.json pointer so
      teammates know to install the global core ($REPO_URL).
-  3. Commit PIPELINE.md + .claude/, then  /brainstorm  to start a feature.
+  3. Commit PIPELINE.md + .claude/, then  /cohorte-brainstorm  to start a feature.
 
-Code retrieval (Serena — the default provider /init-pipeline wires per repo):
+Code retrieval (Serena — the default provider /cohorte-init-pipeline wires per repo):
   uv tool install -p 3.13 serena-agent   # once per machine
   Make sure ~/.local/bin is on PATH (uv tool update-shell) — otherwise the
   registered MCP server silently fails to start.
 
 Global kanban config, user-scoped — optional:
   · One consolidated file: ~/.claude/cohorte.config.yaml (don't hand-edit it).
-  · /init-pipeline (new project) and /update-pipeline (existing) wire it for you: creating +
+  · /cohorte-init-pipeline (new project) and /cohorte-update-pipeline (existing) wire it for you: creating +
     syncing an Obsidian kanban board of the pipeline in your shared vault.
 EOF
   exit 0
@@ -326,11 +336,11 @@ if [ "$mode" = "install" ]; then
 
 Next:
   1. Open the project in Claude Code.
-  2. Run  /init-pipeline   — it detects your stack, asks the gaps, and generates
+  2. Run  /cohorte-init-pipeline   — it detects your stack, asks the gaps, and generates
      PIPELINE.md + renders one implementer agent per surface.
-  3. Commit PIPELINE.md, then  /brainstorm  to start a feature.
+  3. Commit PIPELINE.md, then  /cohorte-brainstorm  to start a feature.
 
-Code retrieval (Serena — the default provider /init-pipeline wires per repo):
+Code retrieval (Serena — the default provider /cohorte-init-pipeline wires per repo):
   uv tool install -p 3.13 serena-agent   # once per machine
   Make sure ~/.local/bin is on PATH (uv tool update-shell) — otherwise the
   registered MCP server silently fails to start.
@@ -346,6 +356,6 @@ else
   cat <<EOF
 
 ✓ core refreshed to $ver. Your PIPELINE.md, rendered surface agents, gate-config.json and
-  settings.json were left as-is. Re-run /init-pipeline if your stack changed.
+  settings.json were left as-is. Re-run /cohorte-init-pipeline if your stack changed.
 EOF
 fi

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "cohorte",
-  "version": "1.6.0",
-  "description": "Portable, stack-agnostic multi-agent development pipeline for Claude Code — install the core, run /init-pipeline, and it adapts to your project's stack.",
+  "version": "2.0.0",
+  "description": "Portable, stack-agnostic multi-agent development pipeline for Claude Code — install the core, run /cohorte-init-pipeline, and it adapts to your project's stack.",
   "bin": {
     "cohorte": "bin/cli.js"
   },

package/profile/PIPELINE.template.md

@@ -1,9 +1,9 @@
 # PIPELINE.md — <PROJECT_NAME> profile
 
-> **Generated by `/init-pipeline`.** This is the project profile: the single place the
+> **Generated by `/cohorte-init-pipeline`.** This is the project profile: the single place the
 > portable multi-agent pipeline reads for everything stack-specific. The pipeline core
 > under `.claude/` is generic and references THIS file by section — keep project facts
-> here, never hardcoded into agent prompts. Kept current by `/update-pipeline` (reconcile:
+> here, never hardcoded into agent prompts. Kept current by `/cohorte-update-pipeline` (reconcile:
 > new fields are topped up, your values never overwritten). Rendered agent files are
 > regenerated from this profile on every reconcile — customize agents through §Conventions
 > here, never by editing the agent files. Free-form notes belong in `CLAUDE.md`.
@@ -36,15 +36,15 @@ repo:
 # wired. serena = live LSP symbol navigation (default, no index to maintain);
 # graphify = persistent tree-sitter knowledge graph over code + docs (needs an
 # index step + rescans); none = agents fall back to Grep/Glob/Read.
-# Registered by /init-pipeline as a project-scope MCP server (committed .mcp.json).
+# Registered by /cohorte-init-pipeline as a project-scope MCP server (committed .mcp.json).
 retrieval:
   provider: serena                            # serena | graphify | none
 
 # ── surfaces ────────────────────────────────────────────────────────────────
-# One entry per independently-implemented code area. /build dispatches ONE
+# One entry per independently-implemented code area. /cohorte-build dispatches ONE
 # implementer agent per surface, in parallel. Each surface is rendered by
-# /init-pipeline into its own agent file (agent field) with the tools listed.
-# This list GROWS automatically: /build §1.5 adds a surface (and renders its
+# /cohorte-init-pipeline into its own agent file (agent field) with the tools listed.
+# This list GROWS automatically: /cohorte-build §1.5 adds a surface (and renders its
 # agent) when a spec touches a tree no surface owns, or splits a bottleneck
 # surface into specialized sub-surfaces. Keep one owner per tree; shared code
 # (routing/state/DS) is its own single-owner surface. See SCHEMA.md §Specialization.
@@ -61,7 +61,7 @@ surfaces:
     test_cmd: pnpm --filter api test
     # Bridled variants — what agents actually RUN (dot reporter / failures-only /
     # --quiet), so a green run costs lines, not pages. "" ⇒ callers fall back to
-    # `<cmd> 2>&1 | tail -40`. /init-pipeline asks for these; never store a bare
+    # `<cmd> 2>&1 | tail -40`. /cohorte-init-pipeline asks for these; never store a bare
     # `pnpm test` as the thing agents execute.
     test_quiet_cmd: pnpm --filter api test --reporter=dot
     lint_cmd: pnpm --filter api lint
@@ -90,7 +90,7 @@ surfaces:
 
 # ── contract (the only cross-surface sync channel) ──────────────────────────
 contract:
-  enabled: <true | false>                     # false ⇒ no shared contract; skip §2 of /build
+  enabled: <true | false>                     # false ⇒ no shared contract; skip §2 of /cohorte-build
   mechanism: <shared-types-zod | openapi | protobuf | json-schema | none>
   path: packages/shared-types/src             # where <feature_id>.<ext> is authored
   ext: ts
@@ -106,7 +106,7 @@ commands:
   format: pnpm format
   typecheck: pnpm check-types
   test: pnpm test
-  test_quiet: pnpm test --reporter=dot       # bridled variant — what the /review preflight runs
+  test_quiet: pnpm test --reporter=dot       # bridled variant — what the /cohorte-review preflight runs
   # migration commands — omit / leave "" if the project has no DB migrations
   migrate: "cd apps/api && node ace migration:run"
   make_migration: "cd apps/api && node ace make:migration"
@@ -119,11 +119,11 @@ rbac:
 
 # ── design system (optional) ────────────────────────────────────────────────
 design:
-  enabled: <true | false>                     # false ⇒ /align-ds + design gates are no-ops
+  enabled: <true | false>                     # false ⇒ /cohorte-align-ds + design gates are no-ops
   provider: <claude-design | figma | none>
   design_system_project: <uuid-or-id>         # the UI-kit source of truth
   design_project: none                        # legacy fallback for bare-filename design_files only; keep `none` — new specs use full links that carry their own project, so nothing here goes stale on a DS rebuild
-  snapshot_dir: apps/web/design-reference     # committed DS snapshot for /align-ds diff
+  snapshot_dir: apps/web/design-reference     # committed DS snapshot for /cohorte-align-ds diff
   direction: design-to-code                   # NEVER push code→design for a curated DS
   ui_kit_path: apps/web/src/components/ui
   tokens_path: apps/web/src/index.css
@@ -166,7 +166,8 @@ gate:
     - "docker compose"
   # Phase gate: review dispatches require a fresh `.claude/preflight.ok` stamp,
   # written by pipeline/scripts/preflight.sh when typecheck+lint+tests are green —
-  # gate.py "ask"s the dispatch when the stamp is missing, stale, or HEAD moved.
+  # gate.py "ask"s the dispatch when the stamp is missing, stale, or the code changed since.
+  # The stamp is local: keep `.claude/preflight.ok` gitignored, never committed.
   preflight:
     enabled: true
     agents: [review]                          # subagent_types the stamp gates
@@ -176,7 +177,7 @@ gate:
 
 > **Note.** The **kanban** board link is **user-scoped** — NOT configured here. Its facts live in the
 > consolidated `~/.claude/cohorte.config.yaml`, read at runtime (the kanban board is keyed by this
-> profile's `name`). This project profile only governs the dev pipeline (`/brainstorm…/ship`).
+> profile's `name`). This project profile only governs the dev pipeline (`/cohorte-brainstorm…/cohorte-ship`).
 
 ---
 
@@ -205,18 +206,18 @@ gate:
 
 ---
 
-## Design brief note (feeds `/spec` §8 and Claude Design)
+## Design brief note (feeds `/cohorte-spec` §8 and Claude Design)
 
 - <design system name + primitives to use · mobile-first · copy language · brand/theming constraints>
 - A feature lists its design pages in the spec front-matter `design_files` as **full links** of the form
   `https://claude.ai/design/p/<projectId>?file=<file>` — each carries its own project (`/p/<projectId>`)
   and page (`?file=`), so an agent extracts both and reads it via `DesignSync get_file(<projectId>,
-  <file>)`. Paste the link at `/build`'s design gate. No stored project id ⇒ a design-system rebuild
+  <file>)`. Paste the link at `/cohorte-build`'s design gate. No stored project id ⇒ a design-system rebuild
   (new project) just means pasting the new links. (Bare file names are legacy, resolved in `design_project`.)
 
 ---
 
-## Personas for `/brainstorm` (optional — the panel)
+## Personas for `/cohorte-brainstorm` (optional — the panel)
 
 <Panel members with a job AND a personality who challenge the idea from their angle and
 disagree with each other. Include a role-coverage guard if `rbac.enabled`. Example:>