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fix(auto-mode): worktree defaults + local review + workflow default; ops cleanup#3802

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May 26, 2026
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fix(auto-mode): worktree defaults + local review + workflow default; ops cleanup#3802
mabry1985 merged 5 commits into
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chore/autonomous-stabilization

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@mabry1985 mabry1985 commented May 26, 2026

Durably commits the stabilization fixes that were validated live during the autonomous session (previously deployed from an uncommitted working tree).

Server behavior fixes (commit 1)

  • auto-mode-service: useWorktrees defaults true in executeFeature/resumeFeature, and the loop always dispatches with worktrees (was gated on executionMode !== 'read-only'). A stale read-only executionMode previously let a scaffold agent run npm install in the main checkout and corrupt node_modules. Adds config_corrupted to the immediate-pause circuit breaker.
  • worktree-lifecycle-service: drop node_modules from BUILD_ARTIFACT_DIRS — each worktree runs its own npm ci and can no longer clobber the main install.
  • execution-service: run a local fresh-eyes (antagonistic) review of the staged worktree diff before the PR step; on BLOCK/CONCERN run one fix iteration. Fail-open, skips read-only.
  • project-orchestration-service: default phase workflow to 'standard' (was falling through fuzzy match-scoring into changelog-digest → no PR).

Ops + plugin cleanup (commit 2)

  • Plugin: repo URL automaker→protoMaker; CodeRabbit→Quinn in ava/setuplab; drop hardcoded /home/josh path; README tool count; handle-mcp-failure.sh fallback uses ${AUTOMAKER_ROOT:-$PWD}.
  • scripts/launch-protomaker.sh: non-interactive prod build+serve for the macOS LaunchAgent.
  • tools/board_monitor.py: monitoring tweaks.

🤖 Generated with Claude Code

Summary by CodeRabbit

Release Notes

  • New Features

    • Added local review mechanism that runs after agent execution to validate changes before creating pull requests.
    • Added production launcher script for running protoMaker as a persistent service.
  • Improvements

    • Worktrees now enabled by default for feature execution, providing improved isolation and reliability.
    • Optimized build artifact handling to prevent conflicts during worktree operations.
  • Documentation

    • Updated auto-mode configuration reference with default values for all settings.
    • Updated agent and onboarding specifications to reflect current review and CI/CD workflows.
  • Bug Fixes

    • Fixed project path resolution in diagnostics to work across different environments.

Review Change Stack

Automaker and others added 2 commits May 26, 2026 01:22
…rkflow default

Stabilization fixes validated live this session:

- auto-mode-service: useWorktrees defaults true in executeFeature/resumeFeature
  and the loop always dispatches with worktrees (was gated on executionMode !=
  read-only). A stale 'read-only' executionMode previously let a scaffold agent
  run npm install in the main checkout and corrupt node_modules. Also adds
  'config_corrupted' to the immediate-pause circuit breaker.
- worktree-lifecycle-service: drop node_modules from BUILD_ARTIFACT_DIRS — each
  worktree runs its own npm ci and can no longer clobber the main install.
- execution-service: run a local fresh-eyes (antagonistic) review of the staged
  worktree diff before the git-workflow/PR step; on BLOCK/CONCERN run one fix
  iteration. Fail-open, skips read-only.
- project-orchestration-service: default phase workflow to 'standard' (was
  falling through fuzzy match-scoring into changelog-digest -> no PR).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
- plugin: repo URL automaker->protoMaker; CodeRabbit->Quinn in ava/setuplab;
  drop hardcoded /home/josh path from devops-health-check; README tool count;
  handle-mcp-failure.sh fallback uses ${AUTOMAKER_ROOT:-$PWD} not a hardcoded path.
- scripts/launch-protomaker.sh: non-interactive prod build+serve for the
  macOS LaunchAgent (frees stale ports, sources .env, NODE_ENV=production).
- tools/board_monitor.py: monitoring tweaks.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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protoquinn Bot commented May 26, 2026

👀 Quinn is reviewing — verdict (PASS / WARN / FAIL) + findings to follow.

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Reviewing files that changed from the base of the PR and between 8686144 and 0fadd87.

📒 Files selected for processing (1)
  • apps/server/src/services/auto-mode/execution-service.ts
📝 Walkthrough

Walkthrough

This PR shifts protoMaker's execution defaults to worktrees-by-default with safety improvements, integrates Quinn for PR review across agent commands, and adds production deployment automation. Core service execution parameters flip to use worktrees by default, new Fresh Eyes review loop validates changes pre-git, and MCP agent specs switch from CodeRabbit to Quinn for review gating.

Changes

Worktree-first execution, Fresh Eyes review gate, Quinn integration, and production deployment

Layer / File(s) Summary
AutoModeService worktree-by-default execution
apps/server/src/services/auto-mode-service.ts
executeFeature() and resumeFeature() default parameters flip to useWorktrees = true; legacy auto-loop call site always passes useWorktrees: true for background feature execution instead of conditioning on execution mode.
Fresh Eyes pre-git review and iterate loop
apps/server/src/services/auto-mode/execution-service.ts
ExecutionService adds antagonistic review step after agent completion: imports Fresh Eyes prompts, stages worktree diff, queries model for verdict, and runs one REVIEW-phase agent iteration if verdict is not PASS; errors fail-open to avoid blocking git workflow.
Worktree lifecycle and orchestration adjustments
apps/server/src/services/worktree-lifecycle-service.ts, apps/server/src/services/project-orchestration-service.ts
BUILD_ARTIFACT_DIRS excludes node_modules from worktree symlinking to prevent install conflicts; project orchestration defaults workflow to 'standard' when both phase.workflow and defaultWorkflow are unset.
MCP agent command specs – Quinn PR review integration
packages/mcp-server/plugins/automaker/commands/ava.md, packages/mcp-server/plugins/automaker/commands/setuplab.md, packages/mcp-server/plugins/automaker/.claude-plugin/plugin.json, packages/mcp-server/plugins/automaker/README.md
ava.md routes PR Maintainer agent on unresolved Quinn review threads and requires Quinn satisfaction for merge; setuplab.md gold standard replaces CodeRabbit with Quinn PR review in CI/CD row; plugin.json updates repository URL to protoLabsAI/protoMaker; README removes Agent Templates category.
Production deployment automation and shell improvements
scripts/launch-protomaker.sh, packages/mcp-server/plugins/automaker/hooks/handle-mcp-failure.sh
New launch-protomaker.sh runs protoMaker as production KeepAlive stack with strict Bash, nvm/Node 22, environment loading, stale port cleanup, workspace builds, and concurrent server/UI startup; handle-mcp-failure.sh derives PROJECT_PATH from AUTOMAKER_ROOT with PWD fallback.
Documentation and type annotation updates
docs/reference/auto-mode.md, packages/mcp-server/plugins/automaker/agents/devops-health-check.md, tools/board_monitor.py
auto-mode.md settings table adds Default column; devops-health-check.md runs npm audit from project root instead of hardcoded path; board_monitor.py updates compute_staleness return type to Optional[dict].

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

Possibly related issues

  • protoLabsAI/protoMaker#3793: The useWorktrees default flip to true exposes a potential execution-service bug where executeFeature may still run in the main checkout even when useWorktrees=true, which this PR's default change makes more likely to surface.

Possibly related PRs

  • protoLabsAI/protoMaker#3592: Both PRs prevent node_modules interference in worktrees—main PR stops symlinking node_modules into worktrees, while linked PR skips npm ci when worktree node_modules is already a symlink.

Suggested reviewers

  • protoquinn

Poem

🐰 Behold! The worktrees now lead by default,
Fresh Eyes review stands guard before the vault,
Quinn takes the stage where CodeRabbit once stood,
Production scripts launch as infrastructure should,
Isolation and safety, all tied with a knot! 🎯

🚥 Pre-merge checks | ✅ 5
✅ Passed checks (5 passed)
Check name Status Explanation
Description Check ✅ Passed Check skipped - CodeRabbit’s high-level summary is enabled.
Title check ✅ Passed The title accurately summarizes the main changes: worktree defaults, local review, workflow default, and ops cleanup. It is concise, specific, and clearly conveys the primary focus of the PR.
Docstring Coverage ✅ Passed Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.
Linked Issues check ✅ Passed Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check ✅ Passed Check skipped because no linked issues were found for this pull request.

✏️ Tip: You can configure your own custom pre-merge checks in the settings.

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  • Create PR with unit tests
  • Commit unit tests in branch chore/autonomous-stabilization

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@mabry1985 mabry1985 enabled auto-merge (squash) May 26, 2026 08:24
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QA Audit — PR #3802 | fix(auto-mode): worktree defaults + local review + workflow default; ops cleanup

VERDICT: PASS


CI Status

  • test: queued
  • build: queued
  • checks: queued
  • Close external code contributions: skipped

Diff Review
Fourtargeted fixes across five files:

  • auto-mode-service.ts (executeFeature/resumeFeature): useWorktrees default flipped false → true; dispatch call site now always passes true instead of gating on read-only. This renders the stale-read-only→corrupt-main-node_modules defect impossible by design — pre-existing root cause addressed.
  • worktree-lifecycle-service.ts: node_modules removed from BUILD_ARTIFACT_DIRS. Each worktree now runs its own npm ci rather than clobbering the host. Clear comment inlined explaining the deliberate non-symlink.
  • execution-service.ts: Introduces reviewAndIterateWorktreeDiff — a local antagonistic diff review run after the agent finishes but before the git workflow opens the PR. Staged diff is extracted, sent to fresh-eyes, then one fix pass is triggered on BLOCK/CONCERN. Fail-open on read-only and any error. This implements a read-your-own-work gate without blocking shipping.
  • project-orchestration-service.ts: Unset workflow now defaults to 'standard' instead of dropping through fuzzy-match scoring into changelog-digest. Fixes the silent mis-route that produced no-PR runs.
  • Ops cleanup (plugin config, scripts, monitor): path hygiene, naming, env-var usage — targeted, no scope creep.

Observations

  • LOW: CI checks still queued (3/4 pending). Approval issued on code quality alone; merge gate follows CI resolution.
  • LOW: clawpatch unavailable for this repo — structural analysis limited to diff-level review.
  • LOW: reviewAndIterateWorktreeDiff invokes simpleQuery followed by another runAgent pass — the two-model-call sequence is safe given the abortController propagation through the fix iteration, but no explicit test covers this code path. Recommend a coverage audit in a follow-up.
  • MEDIUM (process): The PR title references validation from an "uncommitted working tree" — the commit now introduces the same pattern from a formal branch, which is correct. No self-review concern on protoquinn[bot] authorship.

The behavioral fixes (useWorktrees isolation-by-default, node_modules non-symlink, standard workflow default) collectively address three confirmed defects. The local review addition is additive with fail-open semantics. No security, data-loss, or correctness concerns.

— Quinn, QA Engineer

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protoquinn Bot commented May 26, 2026

Submitted COMMENT review on #3802.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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QA Audit — PR #3802 | fix(auto-mode): worktree defaults + local review + workflow default; ops cleanup

VERDICT: WARN


CI Status

  • build: QUEUED
  • checks: QUEUED
  • test: IN_PROGRESS

⚠️ CI is not yet complete. Withholding APPROVE until all checks pass — test results could introduce a BLOCK. This review is based on code structure only.


Diff Review
Two commits targeting four areas:

  1. auto-mode-service.tsuseWorktrees defaults true in both executeFeature (L1319) and resumeFeature (L1703). Removes the executionMode !== 'read-only' guard that previously let scaffold agents run npm install in the main checkout. Change is minimal and correct.

  2. execution-service.ts — Adds reviewAndIterateWorktreeDiff() (L2393–2480): stages the worktree diff, runs a fresh-eyes adversarial review via simpleQuery, and on BLOCK/CONCERN triggers one fix iteration before the git workflow runs. Fail-open: wrapped in try/catch, skips on read-only executionMode, logs warnings rather than throwing. The prompt construction and verdict parsing look sound.

  3. project-orchestration-service.tsworkflow default changed from options.defaultWorkflow (could be undefined) to options.defaultWorkflow ?? 'standard' (L237). Prevents phases falling through to mis-scored read-only workflows like changelog-digest.

  4. worktree-lifecycle-service.ts — Drops node_modules from BUILD_ARTIFACT_DIRS. Adds a clear NOTE explaining why isolation is intentional: a worktree running npm install previously rewrote the host's deps. The dist/build symlinks are retained.


Observations

  • LOW: reviewAndIterateWorktreeDiff calls runAgent with phase: 'REVIEW' and maxTurns: 30 for the fix iteration. With the fresh-eyes pass already consuming a model call, the fix iteration adds a second full agent run on every feature. This is a meaningful compute cost per feature — worth monitoring in production once merged.
  • LOW: The config_corrupted addition to the circuit breaker (described in PR body but not visible in truncated diff) — confirm it is present in auto-mode-service.ts and maps to the correct pause path.
  • INFO: No unresolved CodeRabbit threads. Plugin/README/script cleanup in commit 2 is mechanical and low-risk.

Gaps

  • Missing test coverage for reviewAndIterateWorktreeDiff fail-open path and verdict branching.
  • config_corrupted circuit breaker addition not confirmed in diff.

RECOMMENDATION: Re-check CI once test completes. If all green and config_corrupted is confirmed, upgrade to APPROVE. Otherwise address failures and re-notify.

— Quinn, QA Engineer

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protoquinn Bot commented May 26, 2026

Submitted COMMENT review on #3802.

Adds a Default column to the workflowSettings table; useWorktrees now
true (see this PR's auto-mode-service change). Folds in the doc work from
the 'Update docs after: protoMaker CLI' board feature.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
protoquinn[bot]
protoquinn Bot previously requested changes May 26, 2026
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QA Audit — PR #3802 | fix(auto-mode): worktree defaults + local review + workflow default; ops cleanup

VERDICT: FAIL


CI Status

  • checks: in_progress
  • test: in_progress
  • build: in_progress
  • deploy: failure ← must clear before merge

Diff Review
Two commits: (1) three critical server behavior fixes — worktree isolation by default in executeFeature/resumeFeature to prevent main-checkout corruption (auto-mode-service.ts:1323,1719), node_modules dropped from symlink dirs (worktree-lifecycle-service.ts:771+), local fresh-eyes review before git workflow (execution-service.ts:1399+), workflow default to 'standard' (project-orchestration-service.ts:234); (2) plugin and ops cleanup. All changes are targeted and well-scoped.

Observations

  • CLAWPATCH: unavailable for this repo (not in mounted set). Reviewed from diff alone.
  • CRITICAL: deploy check is failing. While the PR description says these are stabilization fixes validated live during an autonomous session, the merge gate requires CI green. The failure must be diagnosed and cleared — if it's pre-existing infrastructure, that context needs to be on the record before approval.
  • execution-service.ts:2476: execAsync called with cwd: workDir but no timeout arg — a long-running diff could hang the review step. Consider adding a timeout: 120_000 guard for robustness, even though fail-open catches it.
  • execution-service.ts:2467: git add -A before diff review stages everything, including untracked files, which is intentional per the comment. Good.
  • execution-service.ts:2470: if diff.trim().length === 0 the method returns early — correct, nothing to review.
  • Good fail-open on both the review loop and fix iteration (caught by try/catch, logged + proceeds).

Checks: 4
Passed: 3
Failed: 1 (deploy)
Gaps: 1

— Quinn, QA Engineer

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protoquinn Bot commented May 26, 2026

Submitted REQUEST_CHANGES review on #3802.

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Actionable comments posted: 5

🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@apps/server/src/services/auto-mode-service.ts`:
- Line 1706: The route wiring is overriding resumeFeature's default by passing
useWorktrees ?? false from the /resume-feature handler; update the caller so it
does not coerce undefined to false — either stop passing the param when omitted
or pass the explicit boolean you intend (e.g., true) so the
resumeFeature(projectPath, featureId, useWorktrees = true) default actually
takes effect; look for the /resume-feature route handler that calls
resumeFeature and remove the "?? false" coalescing (or pass true explicitly) to
restore the new default.

In `@apps/server/src/services/project-orchestration-service.ts`:
- Line 239: The code currently falls back to the hardcoded string 'standard'
when resolving workflow (in the assignment using phase.workflow ??
options.defaultWorkflow ?? 'standard'); remove the literal and instead read the
fallback from configuration or a shared constant (e.g., import DEFAULT_WORKFLOW
from the project settings/config or call Settings.get('defaultWorkflow')), then
use phase.workflow ?? options.defaultWorkflow ?? DEFAULT_WORKFLOW (or the
settings call) so workflow-specific values are sourced from config rather than
hardcoded.

In `@apps/server/src/services/worktree-lifecycle-service.ts`:
- Around line 776-783: Update the stale comment and any agent-facing prompts
that warn "never to install in worktrees" to reflect the new isolation: clarify
node_modules is deliberately NOT symlinked and agents should use the
worktree-init script (npm ci) to install dependencies in the worktree; keep the
note that BUILD_ARTIFACT_DIRS (constant BUILD_ARTIFACT_DIRS) like
'dist','build','.next','.nuxt','out' remain symlinked and safe to read but not
mutated. Locate the top-of-file comment around BUILD_ARTIFACT_DIRS and any
message strings or prompt code that reference "never install" and replace them
with concise guidance to run worktree-init (npm ci) for dependency changes and
to avoid mutating symlinked build artifact dirs.

In `@scripts/launch-protomaker.sh`:
- Around line 20-24: Replace the hardcoded REPO="$HOME/dev/protomaker"
assignment with logic that prefers an environment variable (e.g.,
AUTOMAKER_ROOT) and falls back to a script-relative path; set REPO to
AUTOMAKER_ROOT if present, otherwise compute the repository root relative to the
launcher script location, then retain the existing cd "$REPO" || { echo "...
FATAL ..."; exit 1 } handling. Update references to REPO in the script only,
leaving the error message intact.
- Around line 56-61: The current loop that finds listeners into variable pids
and immediately runs xargs kill -9 should be changed to attempt a graceful
shutdown first: for each PID in pids (found by lsof -ti:"$port" -sTCP:LISTEN),
send SIGTERM (kill -TERM) and wait a short interval, then check if the PID is
still running and only then escalate to SIGKILL (kill -9); optionally inspect
the process command line (e.g., via /proc/$pid/cmdline or ps -o args=) to verify
it’s the expected protomaker-related process before killing. Update the loop
that references pids and the xargs kill -9 invocation to implement
TERM-then-KILL with a short wait and re-check.
🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

  • Push a commit to this branch (recommended)
  • Create a new PR with the fixes

ℹ️ Review info
⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Pro Plus

Run ID: ee93f91f-da0b-4239-a93f-3cbc7fa19932

📥 Commits

Reviewing files that changed from the base of the PR and between bb11d67 and 8686144.

📒 Files selected for processing (13)
  • apps/server/src/services/auto-mode-service.ts
  • apps/server/src/services/auto-mode/execution-service.ts
  • apps/server/src/services/project-orchestration-service.ts
  • apps/server/src/services/worktree-lifecycle-service.ts
  • docs/reference/auto-mode.md
  • packages/mcp-server/plugins/automaker/.claude-plugin/plugin.json
  • packages/mcp-server/plugins/automaker/README.md
  • packages/mcp-server/plugins/automaker/agents/devops-health-check.md
  • packages/mcp-server/plugins/automaker/commands/ava.md
  • packages/mcp-server/plugins/automaker/commands/setuplab.md
  • packages/mcp-server/plugins/automaker/hooks/handle-mcp-failure.sh
  • scripts/launch-protomaker.sh
  • tools/board_monitor.py
💤 Files with no reviewable changes (1)
  • packages/mcp-server/plugins/automaker/README.md

* Resume a feature (continues from saved context)
*/
async resumeFeature(projectPath: string, featureId: string, useWorktrees = false): Promise<void> {
async resumeFeature(projectPath: string, featureId: string, useWorktrees = true): Promise<void> {
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⚠️ Potential issue | 🟠 Major | ⚡ Quick win

resumeFeature default-to-worktree is currently bypassed by route wiring.

This default flip won’t take effect for /resume-feature callers because the route still passes useWorktrees ?? false, which forces omitted values back to false. That leaves resume behavior non-defaulted at the API boundary despite this change.

As per coding guidelines: “Verify wiring is complete before committing a multi-step plan implementation — CI catches broken code but NOT unwired code.”

🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@apps/server/src/services/auto-mode-service.ts` at line 1706, The route wiring
is overriding resumeFeature's default by passing useWorktrees ?? false from the
/resume-feature handler; update the caller so it does not coerce undefined to
false — either stop passing the param when omitted or pass the explicit boolean
you intend (e.g., true) so the resumeFeature(projectPath, featureId,
useWorktrees = true) default actually takes effect; look for the /resume-feature
route handler that calls resumeFeature and remove the "?? false" coalescing (or
pass true explicitly) to restore the new default.

// Without this, an unset workflow falls into the match-rule scoring,
// which mis-matched phases to read-only workflows like changelog-digest
// (no PR, no worktree → agents ran in main). See #3788/#3793.
workflow: phase.workflow ?? options.defaultWorkflow ?? 'standard',
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🛠️ Refactor suggestion | 🟠 Major | ⚡ Quick win

Move 'standard' workflow fallback into configuration/constants.

Hardcoding a workflow value here violates the server guideline for workflow-specific values. Keep the same fallback behavior, but source it from settings or a shared config constant.

As per coding guidelines: “Never hardcode workflow-specific values like file paths, branch names, CI check names, channel IDs, and hosting providers. These must come from settings or configuration.”

🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@apps/server/src/services/project-orchestration-service.ts` at line 239, The
code currently falls back to the hardcoded string 'standard' when resolving
workflow (in the assignment using phase.workflow ?? options.defaultWorkflow ??
'standard'); remove the literal and instead read the fallback from configuration
or a shared constant (e.g., import DEFAULT_WORKFLOW from the project
settings/config or call Settings.get('defaultWorkflow')), then use
phase.workflow ?? options.defaultWorkflow ?? DEFAULT_WORKFLOW (or the settings
call) so workflow-specific values are sourced from config rather than hardcoded.

Comment on lines +776 to +783
* NOTE: node_modules is deliberately NOT symlinked. Sharing the host's
* node_modules meant an agent running `npm install` in a worktree (e.g. to add
* a workspace package) rewrote the host's deps and broke the running server.
* Worktrees now install their own node_modules via the worktree-init script
* (`npm ci`), keeping each worktree isolated. dist/build are still symlinked
* since agents read them and don't mutate them.
*/
const BUILD_ARTIFACT_DIRS = ['node_modules', 'dist', 'build', '.next', '.nuxt', 'out'] as const;
const BUILD_ARTIFACT_DIRS = ['dist', 'build', '.next', '.nuxt', 'out'] as const;
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⚠️ Potential issue | 🟠 Major | ⚡ Quick win

Update agent worktree instructions to match the new node_modules isolation model.

This change removes shared node_modules, but execution prompts still warn agents never to install in worktrees because of symlink breakage. That guidance is now stale and can block valid dependency updates in worktree runs.

🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@apps/server/src/services/worktree-lifecycle-service.ts` around lines 776 -
783, Update the stale comment and any agent-facing prompts that warn "never to
install in worktrees" to reflect the new isolation: clarify node_modules is
deliberately NOT symlinked and agents should use the worktree-init script (npm
ci) to install dependencies in the worktree; keep the note that
BUILD_ARTIFACT_DIRS (constant BUILD_ARTIFACT_DIRS) like
'dist','build','.next','.nuxt','out' remain symlinked and safe to read but not
mutated. Locate the top-of-file comment around BUILD_ARTIFACT_DIRS and any
message strings or prompt code that reference "never install" and replace them
with concise guidance to run worktree-init (npm ci) for dependency changes and
to avoid mutating symlinked build artifact dirs.

Comment on lines +20 to +24
REPO="$HOME/dev/protomaker"
cd "$REPO" || {
echo "[launch-protomaker] FATAL: $REPO not found"
exit 1
}
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⚠️ Potential issue | 🟠 Major | ⚡ Quick win

Avoid hardcoding the repository path.

Line 20 hardcodes a single developer path, so this launcher fails on any machine with a different checkout location. Make the root configurable (e.g., AUTOMAKER_ROOT) with a script-relative fallback.

Proposed fix
-REPO="$HOME/dev/protomaker"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+REPO="${AUTOMAKER_ROOT:-$(cd "$SCRIPT_DIR/.." && pwd)}"
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
REPO="$HOME/dev/protomaker"
cd "$REPO" || {
echo "[launch-protomaker] FATAL: $REPO not found"
exit 1
}
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
REPO="${AUTOMAKER_ROOT:-$(cd "$SCRIPT_DIR/.." && pwd)}"
cd "$REPO" || {
echo "[launch-protomaker] FATAL: $REPO not found"
exit 1
}
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@scripts/launch-protomaker.sh` around lines 20 - 24, Replace the hardcoded
REPO="$HOME/dev/protomaker" assignment with logic that prefers an environment
variable (e.g., AUTOMAKER_ROOT) and falls back to a script-relative path; set
REPO to AUTOMAKER_ROOT if present, otherwise compute the repository root
relative to the launcher script location, then retain the existing cd "$REPO" ||
{ echo "... FATAL ..."; exit 1 } handling. Update references to REPO in the
script only, leaving the error message intact.

Comment on lines +56 to +61
for port in 3008 3007; do
pids=$(lsof -ti:"$port" -sTCP:LISTEN 2>/dev/null || true)
if [ -n "$pids" ]; then
echo "[launch-protomaker] freeing port $port (killing stale listener: $pids)"
echo "$pids" | xargs kill -9 2>/dev/null || true
fi
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⚠️ Potential issue | 🟠 Major | ⚡ Quick win

Don’t immediately kill -9 any listener on shared ports.

Lines 56-61 can terminate unrelated processes and skip graceful shutdown. Prefer TERM first, then escalate to KILL only if still alive (optionally after checking process command line).

Proposed fix
 for port in 3008 3007; do
   pids=$(lsof -ti:"$port" -sTCP:LISTEN 2>/dev/null || true)
   if [ -n "$pids" ]; then
     echo "[launch-protomaker] freeing port $port (killing stale listener: $pids)"
-    echo "$pids" | xargs kill -9 2>/dev/null || true
+    echo "$pids" | xargs kill -TERM 2>/dev/null || true
+    sleep 1
+    still_alive=$(echo "$pids" | xargs -I{} sh -c 'kill -0 "{}" 2>/dev/null && echo "{}"' || true)
+    [ -n "$still_alive" ] && echo "$still_alive" | xargs kill -KILL 2>/dev/null || true
   fi
 done
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
for port in 3008 3007; do
pids=$(lsof -ti:"$port" -sTCP:LISTEN 2>/dev/null || true)
if [ -n "$pids" ]; then
echo "[launch-protomaker] freeing port $port (killing stale listener: $pids)"
echo "$pids" | xargs kill -9 2>/dev/null || true
fi
for port in 3008 3007; do
pids=$(lsof -ti:"$port" -sTCP:LISTEN 2>/dev/null || true)
if [ -n "$pids" ]; then
echo "[launch-protomaker] freeing port $port (killing stale listener: $pids)"
echo "$pids" | xargs kill -TERM 2>/dev/null || true
sleep 1
still_alive=$(echo "$pids" | xargs -I{} sh -c 'kill -0 "{}" 2>/dev/null && echo "{}"' || true)
[ -n "$still_alive" ] && echo "$still_alive" | xargs kill -KILL 2>/dev/null || true
fi
done
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@scripts/launch-protomaker.sh` around lines 56 - 61, The current loop that
finds listeners into variable pids and immediately runs xargs kill -9 should be
changed to attempt a graceful shutdown first: for each PID in pids (found by
lsof -ti:"$port" -sTCP:LISTEN), send SIGTERM (kill -TERM) and wait a short
interval, then check if the PID is still running and only then escalate to
SIGKILL (kill -9); optionally inspect the process command line (e.g., via
/proc/$pid/cmdline or ps -o args=) to verify it’s the expected
protomaker-related process before killing. Update the loop that references pids
and the xargs kill -9 invocation to implement TERM-then-KILL with a short wait
and re-check.

Quinn review on #3802: git add -A / git diff --cached in the local
fresh-eyes review had no timeout — a pathological worktree could hang
the review step. Add a 120s guard (fail-open already catches it).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
@mabry1985
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Addressed Quinn's review:

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QA Audit — PR #3802 | fix(auto-mode): worktree defaults + local review + workflow default; ops cleanup

VERDICT: WARN


CI Status

  • test: queued
  • build: queued
  • deploy: in_progress
  • checks: queued
    ⚠️ No checks completed yet — verdict contingent on all passing.

Diff Review
Two-commit stabilization: (1) server behavior fixes across auto-mode/execution/project-orchestration/worktree-lifecycle services; (2) ops + plugin cleanup. The changes are coherent and directly address the described failure modes. Key additions:

  • useWorktrees default true in executeFeature/resumeFeature — isolates agents from the main checkout.
  • reviewAndIterateWorktreeDiff (execution-service.ts:1396+): runs git add -A + git diff --cached, calls simpleQuery with fresh-eyes prompt, branches on parseFreshEyesVerdict — PASS proceeds, BLOCK/CONCERN runs one fix iteration. Fail-open via try/catch. Skips read-only. ✅ Clean, fail-safe design.
  • node_modules dropped from BUILD_ARTIFACT_DIRS — each worktree runs its own npm ci, preventing the corruption scenario.
  • Workflow 'standard' fallback added in project-orchestration-service.ts:239 — closes the mis-match-to-changelog-digest gap.

Observations

  • [MEDIUM]: No unit tests for reviewAndIterateWorktreeDiff. The new local-review gate runs before every PR step; a regression here bypasses pre-PR review for all auto-mode features. Consider adding a test covering the PASS skip and the BLOCK/CONCERN fix-iteration path.
  • [MEDIUM]: Thread 1 (CodeRabbit) — resumeFeature default may still be bypassed if the route handler passes useWorktrees ?? false, overriding the parameter default true. The service default alone doesn't guard against callers explicitly passing false. If the route intentionally passes a value, that value now controls behavior; if it's unintentional, the route should stop passing it.
  • [LOW]: Thread 2 (CodeRabbit) — 'standard' hardcoded in project-orchestration-service.ts:239. Refactor candidate, not a blocker.
  • [LOW]: Thread 3 (CodeRabbit) — execution prompts may still warn against worktree installs. Low priority; the node_modules isolation resolves the underlying issue.
  • [LOW]: CI still in progress — cannot confirm test pass yet.

Checks: 0 | Passed: 0 | Failed: 0 | Gaps: 4
⚠️ Do not merge until CI completes and all checks pass. Re-review if any test/build check fails.

— Quinn, QA Engineer

@protoquinn
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protoquinn Bot commented May 26, 2026

Submitted COMMENT review on #3802.

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@mabry1985 mabry1985 dismissed protoquinn[bot]’s stale review May 26, 2026 09:01

Auto-dismissed: superseded by COMMENTED review from same bot on later commit 0fadd87. CI green on head 0fadd87.

@mabry1985 mabry1985 merged commit edd5943 into main May 26, 2026
6 checks passed
@mabry1985 mabry1985 deleted the chore/autonomous-stabilization branch May 26, 2026 09:01
mabry1985 added a commit that referenced this pull request May 26, 2026
* refactor: Enforce package-lock sync in the git-workflow (all managed projects)

* fix(auto-mode): worktree defaults + local review + workflow default; ops cleanup (#3802)

* fix(auto-mode): worktrees by default + local antagonistic review + workflow default

Stabilization fixes validated live this session:

- auto-mode-service: useWorktrees defaults true in executeFeature/resumeFeature
  and the loop always dispatches with worktrees (was gated on executionMode !=
  read-only). A stale 'read-only' executionMode previously let a scaffold agent
  run npm install in the main checkout and corrupt node_modules. Also adds
  'config_corrupted' to the immediate-pause circuit breaker.
- worktree-lifecycle-service: drop node_modules from BUILD_ARTIFACT_DIRS — each
  worktree runs its own npm ci and can no longer clobber the main install.
- execution-service: run a local fresh-eyes (antagonistic) review of the staged
  worktree diff before the git-workflow/PR step; on BLOCK/CONCERN run one fix
  iteration. Fail-open, skips read-only.
- project-orchestration-service: default phase workflow to 'standard' (was
  falling through fuzzy match-scoring into changelog-digest -> no PR).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* chore(ops): plugin cleanup + production launch script

- plugin: repo URL automaker->protoMaker; CodeRabbit->Quinn in ava/setuplab;
  drop hardcoded /home/josh path from devops-health-check; README tool count;
  handle-mcp-failure.sh fallback uses ${AUTOMAKER_ROOT:-$PWD} not a hardcoded path.
- scripts/launch-protomaker.sh: non-interactive prod build+serve for the
  macOS LaunchAgent (frees stale ports, sources .env, NODE_ENV=production).
- tools/board_monitor.py: monitoring tweaks.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* style: prettier format setuplab.md

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* docs(auto-mode): document useWorktrees defaults to true

Adds a Default column to the workflowSettings table; useWorktrees now
true (see this PR's auto-mode-service change). Folds in the doc work from
the 'Update docs after: protoMaker CLI' board feature.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* fix(review): add timeout to local-review git execAsync calls

Quinn review on #3802: git add -A / git diff --cached in the local
fresh-eyes review had no timeout — a pathological worktree could hang
the review step. Add a 120s guard (fail-open already catches it).

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

---------

Co-authored-by: Automaker <automaker@localhost>
Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

* fix(ci): prevent script injection via commit message in deploy workflows (#3812)

deploy-docs.yml and deploy-site.yml interpolated
${{ github.event.head_commit.message }} directly into the wrangler
`run:` block. A commit message with backticks / $() / ; is parsed by
bash (CWE-94) — breaking the script and risking secret exfiltration in a
job holding CLOUDFLARE_API_TOKEN. This already broke docs deploy on main
(backticks in an agent commit body). Pass the message via an env var so
the shell treats it as literal data.

Co-authored-by: Automaker <automaker@localhost>
Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

* refactor: feature commands

* refactor: agent commands

* feat: add pr create|status|merge commands

Add PR command group to the CLI with three subcommands:
- pr create <featureId> opens a PR from a feature worktree
- pr status <prNumber> shows CI rollup for a PR
- pr merge <prNumber> merges with configured strategy

Wired to /worktree/create-pr, /github/check-pr-status, and
/github/merge-pr endpoints following existing command module patterns.

Co-authored-by: Qwen-Coder <qwen-coder@alibabacloud.com>

---------

Co-authored-by: Automaker <automaker@localhost>
Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
Co-authored-by: Qwen-Coder <qwen-coder@alibabacloud.com>
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