fix(make): harden reset against dirty submodule locks

[shunkakinoki]

Summary

• Make make reset hard-reset and force-update submodules so a dirty skills-lock.json cannot block checkout
• Sync submodule URLs recursively
• Bump dotagents to include fix(skills): stop rewriting lock on every install dotagents#183 (stop rewriting the lock on every skills-install)

Test plan

• With a dirty dotagents/skills-lock.json, make reset succeeds and leaves a clean tree
• make git-submodule-sync still updates submodules normally
• make sync no longer dirties dotagents when all skills are already installed

Made with Cursor

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Summary by cubic

Hardened make reset so dirty submodule locks (e.g., dotagents/skills-lock.json) no longer block checkout and the tree ends clean. Also made submodule sync recursive and updated dotagents to stop unnecessary lock rewrites.

• Bug Fixes

  • make reset now hard-resets repo and submodules, cleans submodules, syncs URLs recursively, then force-updates.
  • git-submodule-sync now uses git submodule sync --recursive.

• Dependencies

  • Bumped dotagents to include the skills-install fix that avoids rewriting skills-lock.json when unchanged.

^{Written for commit a7dea1f. Summary will update on new commits.}

[indent-zero]

PR Summary

Hardens make reset so it succeeds even when a submodule has a dirty working tree (specifically the recurring dotagents/skills-lock.json dirtiness that was blocking resets), and bumps dotagents to pick up the upstream fix that stops make sync from re-dirtying the lockfile.

• Makefile reset now runs git reset --hard HEAD, git submodule foreach --recursive 'git reset --hard HEAD && git clean -fd', git submodule sync --recursive, and git submodule update --init --recursive --force instead of just git checkout -- . after git-submodule-sync.
• Makefile git-submodule-sync adds --recursive to git submodule sync for consistency with the recursive update.
• Bumps dotagents submodule from 082de5d → f8b3e29 (fix(skills): stop rewriting lock on every install, dotagents#183), which addresses the root cause of the dirty lockfile.

Issues

2 potential issues found:

• Asymmetric cleanup in make reset: submodules get git clean -fd, but the parent tree does not, so untracked files at the top level survive the reset. Consider adding git clean -fd (or -fdx) at the parent for consistency, or leave as-is if preserving parent untracked files is intentional. → Autofix
• git clean -fd inside submodules leaves gitignored files (build artifacts, caches, generated lockfiles). If make reset is meant to produce a fully pristine tree, use git clean -fdx; if preserving caches is intentional, leaving as-is is fine. → Autofix

CI Checks

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📥 Commits

Reviewing files that changed from the base of the PR and between ef94b8e and a7dea1f.

📒 Files selected for processing (2)

• Makefile
• dotagents

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[indent-zero]

Nit — asymmetric cleanup: The submodule foreach step cleans untracked files inside each submodule with git clean -fd, but there's no equivalent git clean -fd at the parent. git reset --hard HEAD on line 290 only touches tracked/staged files, so someone running make reset expecting a clean tree will still see untracked files at the top level while submodules are pristine. If preserving parent untracked files is intentional (safety net), ignore; otherwise consider adding @git clean -fd here for symmetry.

[indent-zero]

Nit — ignored files retained: git clean -fd does not remove .gitignored files inside submodules. If the intent of make reset is to produce a fully pristine tree (e.g., wipe generated caches/artifacts), use git clean -fdx. If retaining caches is intentional, this is fine as-is.