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Cade's Dotfiles

Home directory is near quota despite `install/scratch.sh` running

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Source: Troubleshooting reference

Symptom: df -H ~ reports the home filesystem close to full even though .local, .cache, and the other DF_LINKS entries are already symlinked to scratch space, and disk-dependent tools (e.g. an MCP server’s cache doctor check) start failing on free-space thresholds.

Root cause: install/scratch.sh only migrates a fixed, named list of cache-shaped directories (DF_LINKS, plus DF_CLAUDE_LINKS/DF_CODEX_LINKS one level under the chezmoi-managed ~/.claude/~/.codex). Two other classes of growth are not covered automatically:

  1. Ad hoc project/output directories created directly under ~ (build trees, bug-repro dumps, scratch clones) — install/dirs.sh already provisions ~/dev, ~/bones, and ~/misc as scratch-backed symlinks for exactly this, but nothing enforces using them; a directory created as ~/<name> instead of ~/misc/<name> sits on the small quota indefinitely.
  2. New subdirectories an app adds after the DF_CODEX_LINKS/DF_CONFIG_LINKS default list was written — e.g. Codex’s db-backups/ (pre-migration SQLite schema-upgrade snapshots) grew unnoticed under ~/.codex for months because the migration list only knew about backups/, a similarly-named but different directory.

Confirm: du -sh --exclude=.local -- ~/.[!.]* ~/* 2>/dev/null | sort -rh | head -20 to find what’s actually large; for a chezmoi-managed dir like ~/.claude or ~/.codex, run du -sh ~/.codex/* ~/.codex/.[!.]* one level down, since the directory itself can’t be a symlink (see the “never symlink a chezmoi-managed directory” gotcha in .claude/rules/install-scripts.md).

Fix: for case 1, move the stray directory under ~/misc/<name> (or ~/dev, ~/bones) and update anything that referenced the old path; going forward, create new project/output directories there directly rather than in ~. For case 2, add the missing subdir name to the relevant _DEFAULT_*_LINKS list in install/scratch.sh and rerun it — Codex/Claude Code must not be running at the time, since scratch.sh refuses to migrate ~/.codex while a process holds its files open (a live app-server can otherwise keep writing to an unlinked inode across the migration).