Add .keep file to persist directory permissions #108
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The .deepwork/tmp directory is referenced in Claude Code permissions but wasn't being tracked by git, causing the directory to not exist when Claude Code starts in a fresh clone. This adds a .keep file to ensure the directory persists in version control and updates the install process to create it automatically.
Include .last_head_ref alongside .last_work_tree in the .gitignore that gets created during deepwork install.
.gitkeep is the more widely recognized convention for placeholder files that ensure directories are tracked by git.
Consolidates all .deepwork-related gitignore rules into .deepwork/.gitignore where they belong. This avoids conflicts with users' root .gitignore files and keeps the ignore rules with the directory they apply to.
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