Uninstalling

Remove harness configs firstCopy Anchor Link

The bare apothem command used on this page is the shim that the one-shot installer (channel 3 of the installation guide) writes; it runs once that shim's directory is on PATH. On the other install channels, substitute npx @ahmed-g-gad/apothem for apothem, as the installation guide describes.

Before uninstalling Apothem, remove each harness adapter config to leave your harnesses in a clean state. Run apothem harnesses list to see which adapters are currently installed, then remove them one at a time or use the registry-wide selector:

apothem uninstall --harness claude-code
apothem uninstall --harness cursor --project /path/to/project
apothem uninstall --harness all --project /path/to/project --yes

Pass --yes to skip the per-harness confirmation prompt.

Remove the engineCopy Anchor Link

Removal matches the install channel you used. Channel numbers are those of the install channel table:

• Claude Code plugin (channel 1) — remove the plugin from inside Claude Code: /plugin uninstall apothem@apothem (the marketplace entry can be removed with /plugin marketplace remove ahmed-g-gad/apothem).

• npx (channel 2) — nothing to remove; npx runs from its cache. Clear it with npm cache clean --force if you want the cached copy gone.

• One-shot installer (channel 3) — run the matching uninstall script from the checkout: scripts/installer/uninstall.sh (POSIX) or scripts/installer/uninstall.ps1 (PowerShell). Each script removes the harness named by --harness (-Harness on PowerShell), else APOTHEM_HARNESS, else Claude Code. It also removes the apothem command shim. The source comes from APOTHEM_SOURCE when set, or from APOTHEM_HOME (default $HOME/.apothem). The source stays unless you pass --remove-source (-RemoveSource on PowerShell). That flag deletes only the managed clone at APOTHEM_HOME, and only when it has a .git directory. With the default location, it also deletes the install backups and the ledger under ~/.apothem/. Both prompt before removing the harness configs and the source. --yes (-Yes on PowerShell) skips the prompts. Both refuse unsafe targets.

• VS Code-family extension (channel 4) — run Apothem: Uninstall from the command palette first to remove the harness configs, then remove the extension from the Extensions view or with code --uninstall-extension ahmed-g-gad.apothem-vscode (a copy installed from an earlier apothem.vsix is ahmed-g-gad.apothem). By default the extension runs the engine through npx, so the npx entry above covers the cache.

• Command-line bootstraps (channels 5–7) — remove the extension or plugin with its host tool after the harness configs are gone. The hosts:

  Copy Text

  channel 5   Gemini CLI extension
  channel 6   Qwen Code extension
  channel 7   Codex plugin

  The bootstrap only adds assistant context (a context file, a command, or a skill) that calls the engine through npx, so nothing else remains. The extension hosts of channels 5 and 6 take an uninstall command; for the plugin host of channel 7, uninstall apothem in its plugin browser.

  Copy Text

  gemini extensions uninstall apothem   # channel 5
  qwen extensions uninstall apothem     # channel 6

• Direct engine (channel 8) — nothing to uninstall; delete the clone once the harness configs are removed.

• Backups and state — install backups live under ~/.apothem/backups/ and the install ledger under ~/.apothem/state/. Both stay bounded: after every install, uninstall and rollback Apothem keeps the newest 10 install records per install root and the newest 10 backup sets per harness, and never deletes a backup a kept record still needs, so the last 10 installs can still be rolled back. To keep fewer, run apothem backups prune --keep N (add --dry-run to see what it would remove first); it never removes the backup that rollback of a harness's latest install restores from. Once the engine is removed and you no longer need any of the history, delete ~/.apothem/.

What is NOT removedCopy Anchor Link

• The shared profile YAML at ~/.config/apothem/profile.yaml or --profile PATH is never removed by apothem uninstall.
• Unrelated operator-authored files in harness directories are preserved.
• Entries you added to a shared settings file are preserved: your own permission rules, MCP servers and hook handlers stay. Uninstall removes only the keys and list entries the install ledger records as Apothem's (see Settings).
• The shared data stores under .apothem/ at the install root (memory/, contexts/, learning/) stay while another installed harness at the same root still uses them. Uninstalling the last harness at that root copies each store into ~/.apothem/backups/ first, then removes it with everything in it.
• Plan suites under <project>/.apothem/plans/ (and the legacy <project>/.plans/) are unaffected.

DirectoriesCopy Anchor Link

Uninstall also removes the directories the install created (for example a ~/.claude/ that did not exist before the first install), once they are empty. A directory that still holds a file of yours, or data another installed harness uses, stays. Directories that existed before the install are never removed.

To fully clean up a harness root, remove the harness-native path documented on the harness reference pages after confirming you have backed up any custom rules, helpers, or profile files you want to keep.