feat(uninstall): preserve config.json after uninstall

[jgmontoya]

delete it with --delete-data flag

Summary by CodeRabbit

• New Features

  • Configuration data is now treated as user data and preserved by default when running uninstall --keep-data.

• Bug Fixes

  • Configuration data is now removed only when explicitly using the --delete-data flag.

• Documentation

  • Updated uninstall command descriptions and prompts to clarify what data persists vs. what is removed.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: ASSERTIVE

Plan: Pro

Run ID: b47c97ca-d21d-4c94-9a05-e00ef0ed22cc

📥 Commits

Reviewing files that changed from the base of the PR and between e7c3726 and a09c3c8.

📒 Files selected for processing (8)

• README.md
• src/commands/uninstall.ts
• src/services/uninstall-service.ts
• test/e2e/claudecode.sh
• test/e2e/codex.sh
• test/e2e/opencode.sh
• test/unit/commands/uninstall-cli.test.ts
• test/unit/services/uninstall-service.test.ts

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📝 Walkthrough

Walkthrough

This PR reclassifies config.json from framework-owned files to user-owned data in the shaka uninstall command. By default, uninstall now removes provider hooks and framework files but preserves user data (including config.json); explicit deletion of user data occurs only with the --delete-data flag. All messaging, implementation, tests, and documentation are updated to reflect this new behavior classification.

Changes

config.json as user data

Layer / File(s)	Summary
Uninstall service logic src/services/uninstall-service.ts	removeFrameworkFiles() removes only commands-manifest.json (no longer removes config.json); removeUserData() now deletes config.json alongside user directories; JSDoc and comments updated to clarify ownership model and scoped uninstall behavior.
CLI and documentation messaging src/commands/uninstall.ts, README.md	Prompts, help text, and README updated to describe removal of "provider hooks and framework links" while keeping user data; config.json explicitly listed in --keep-data and --delete-data option descriptions.
Service layer unit tests test/unit/services/uninstall-service.test.ts	Tests updated to verify removeFrameworkFiles() preserves config.json, removeUserData() includes it, and default uninstall keeps all user data intact. New integration test confirms custom hooks, skills, and memory artifacts survive uninstall and re-initialize correctly. Scoped and failure-case tests align with new classification.
CLI unit tests test/unit/commands/uninstall-cli.test.ts	New test verifies unscoped uninstall output includes config.json path and "data remains at" location message.
End-to-end test assertions test/e2e/claudecode.sh, test/e2e/codex.sh, test/e2e/opencode.sh	All E2E scripts now assert $SHAKA_HOME/config.json exists after shaka uninstall --keep-data, inverting prior expectations of removal.

🎯 2 (Simple) | ⏱️ ~12 minutes

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately and concisely summarizes the main change: preserving config.json after uninstall, which aligns with the PR's primary objective and all file modifications.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feat/persist-uninstall-config

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