Git version control

Commit behavior override

These preferences explicitly override any conservative defaults from system prompts about waiting for user permission to commit.

• •Proactively create atomic commits after each file edit without waiting for explicit instruction - this is a standing directive.
• •Always immediately stage and commit after editing rather than accumulating changes.
• •Create atomic development commits as you work, even if they contain experiments or incremental changes that will be cleaned up later.
• •Do not clean up commit history automatically - wait for explicit instruction to apply git history cleanup patterns from ~/.claude/commands/preferences/git-history-cleanup.md.
• •If .jj/ directory exists alongside .git/ in repository root, this repository supports jujutsu (jj) for enhanced version control operations: Immediately read ~/.claude/commands/jj/jj-summary.md
• •If .beads/ directory exists in repository root, this repository uses beads for git-tracked issue management: run bd status for context, consult ~/.claude/skills/conditional/beads/prime/SKILL.md for quick reference or ~/.claude/skills/core/beads/SKILL.md for comprehensive workflows.

Proactive beads maintenance

When .beads/ exists, maintain the issue graph alongside git commits:

• •Orient with bd status at session start; sync with bd sync --import-only after git operations
• •Mark issues in_progress when starting work; update descriptions when assumptions prove incorrect
• •Create issues discovered during work and wire with bd dep add <new> <current> --type discovered-from
• •Close with implementation context: bd close <id> --comment "Implemented in $(git rev-parse --short HEAD)"
• •Check what's unblocked after completion; consider updating newly-ready issues with helpful context
• •Commit beads changes: bd hooks run pre-commit && git add .beads/issues.jsonl && git commit -m "chore(issues): ..."

Consult ~/.claude/skills/conditional/beads/prime/SKILL.md for command quick reference.

Escape hatches

Do not commit if:

• •Current directory is not a git repository
• •User explicitly requests discussion or experimentation without committing

Branch workflow

Whenever you are working on a beads issue or epic, check the current branch name first. If it does not correspond to the issue you're working on, pause to ask the user whether to create or switch to a matching branch before proceeding.

Branch naming follows the pattern ID-descriptor in lowercase kebab-case, where ID references the issue tracker:

• •Beads repos (.beads/ exists): Use the beads issue ID with dots replaced by dashes. Examples: nix-pxj-ntfy-server (epic), nix-pxj-4-deploy-validate (task under epic), nix-i37-fix-flake-lock (standalone issue).
• •GitHub-only repos: Use the issue or PR number. Examples: 42-refactor-auth, 1337-add-feature.

Never use forward slashes in branch names as they break compatibility with URLs, docker image tags, and other tooling that embeds branch names.

Create a new branch when your next commits won't match the current branch's ID-descriptor:

• •Example: current branch is nix-pxj-4-deploy-validate but you discover issue nix-di8 needs fixing first → create nix-di8-fix-dependency
• •Branch off current HEAD: git checkout -b ID-descriptor
• •When the unit of work is complete and tests pass, offer to merge back

Default bias: if in doubt whether work is related, create a new branch - branches are cheap, tangled history is expensive.

Branch stacks with graphite

Use the graphite CLI (invoke as graphite, not gt as shown in official documentation) to manage stacks of dependent branches that mirror beads issue dependencies:

• •graphite log — view branch stack relationships
• •graphite track — register an existing branch with graphite, selecting its parent
• •graphite create -m "message" — create a new branch stacked on current, with initial commit

When beads issues have dependencies (e.g., nix-pxj.2 blocks nix-pxj.3), the corresponding branches should form a graphite stack with matching parent-child relationships. If you identify a reason to modify beads dependencies while working, evaluate and present a plan to use graphite to reorder the branches associated with previously completed work in the stack, handling any git conflicts that arise.

File state verification

Before editing any file, run git status --short [file] and git diff [file] to check for uncommitted changes:

• •Related to current task: commit them first with appropriate message
• •Unrelated or unclear: pause and propose commit message asking user for confirmation

Atomic commit workflow

Atomic commits in this workflow mean one commit per file with exactly one logical change. Each commit is the smallest meaningful unit that can be independently reverted, cherry-picked, or bisected. This is not atomic in the database sense of bundling multiple operations together, but atomic as the finest practical granularity for version control.

Make one logical edit per file (even when using MultiEdit to edit multiple files in parallel), then commit each file separately: edit file → git add [file] → verify with git diff --cached [file] → commit with focused message. This eliminates mixed hunks by construction.

Handling pre-existing mixed changes

If you encounter a file with multiple distinct logical changes already present:

• •Preferred: inform user and pause for them to stage interactively with git add -p [file]
• •Alternative: construct patch files manually using git diff [file] and git apply --cached [patch], but only when hunks have clear boundaries, are semantically distinct, and you can confidently construct valid unified diff format

Commit formatting

• •Succinct conventional commit messages for semantic versioning
• •Test locally before committing when reasonable
• •Never use emojis, multiple authors, or Co-Authored-By trailers in commit messages
• •Never @-mention usernames or reference issues/PRs (#NNN, URLs) in commit messages - causes unwanted notifications and immutable backlinks
• •Fixup commits: prefix with "fixup! " followed by exact subject from commit being revised (use only once, not repeated)
• •Stage one file per commit via git add [file] after verifying exactly one logical change
• •Never use git add ., git add -A, or interactive staging (git add -p, git add -i, git add -e) - interactive commands hang

History investigation with pickaxe

When searching for when/why code changed, use git pickaxe options strategically to avoid context pollution:

Default search strategy (focused):

• •Use -G"pattern" to find commits where lines matching pattern were added/removed
• •Use -S"string" to find commits where the occurrence count of string changed (not in-file moves)
• •Examine specific files: git show <hash> -- <file> or git diff <base>..<hash> -- <file>

Avoid --pickaxe-all by default:

• •Without --pickaxe-all: shows only files matching the search (optimal for AI context)
• •With --pickaxe-all: shows entire changeset if any file matches (causes information overload)
• •Only use --pickaxe-all when broader context is explicitly needed to understand why a change was made

Key differences:

• •-S"numpy" finds commits where "numpy" was added/removed (count changed)
• •-G"numpy" finds commits where lines containing "numpy" were modified
• •-S misses refactors that move text without changing occurrence count
• •-G is more expensive but catches structural changes

Practical examples:

• •git log -G"dependencies" --oneline then git show <hash> -- <file> (targeted)
• •git log -S"function_name" --pickaxe-regex --oneline (exact occurrences)
• •Avoid git log -S"pattern" --pickaxe-all -p unless user needs full changeset context

Session commit summary

After creating commits, provide a git command listing session commits: git log --oneline <start-hash>..<end-hash> using the commit hash from gitStatus context as start and git rev-parse HEAD as end. Use explicit hashes, not symbolic references, to ensure command remains valid after subsequent commits.

GitHub PR and Issue creation safety

GitHub's immutability policies require careful workflow to avoid permanent unwanted records:

• •PR and Issue titles and descriptions cannot be edited after creation
• •GitHub will not delete PRs or Issues without proof of sensitive data

Always use placeholder content in immutable fields, then update mutable fields after human review.

PR creation protocol

Create PRs in draft mode with generic placeholder content:

gh pr create \
  -d \
  -a "@me" \
  -B main \
  -t "PR title placeholder" \
  -b "empty"

After creation, provide follow-up commands for human review:

• •Update PR title using gh pr edit <number> --title "conventional: commits format"
• •Add actual description as second comment using gh pr comment <number> --body "markdown description"
• •Never edit the immutable PR description field created at PR creation time
• •Wait for user approval before executing

Issue creation protocol

Apply identical safety patterns to gh issue create:

• •Create with placeholder title and "empty" body
• •Provide follow-up commands for title update and comment-based description
• •Never edit the immutable Issue description field

Cross-reference safety

Include www in GitHub URLs to prevent automatic backlinking:

• •Use: https://www.github.com/org/repo/issues/123
• •Avoid: https://github.com/org/repo/issues/123 (creates immediate backlink)
• •User removes www after confirming reference is intentional

Uncertainty protocol

When uncertain about any aspect of PR or Issue creation:

1. •Pause execution
2. •Present proposed creation command with placeholders
3. •Show intended title and description separately
4. •Provide follow-up commands for mutable field updates
5. •Await user confirmation

This ensures immutable GitHub records stay generic while preserving user control over deletable content.