feat(cli): manage plugin capability scopes via command args

[SequeI]

• Add plugin manage support to add/remove capability scopes with:
  • -a/--add-scopes <capability_id>::<scope>
  • -r/--remove-scopes <capability_id>::<scope>
• Enforce mutual exclusivity between -a and -r.
• --dry-run prints only planned changes (no file diffs, no writes).
• --config <path> allows targeting a specific agentup.yml.
• Clear UX messages for added/removed/duplicate/missing scopes & capabilities.

Tests:

• Add manage-only tests covering add/remove, dry-run, duplicates, invalid format, unknown plugin/capability, multi-adds, and missing config path, using a real minimal agentup.yml fixture.

Our commands are a bit of a mess right now as we just add stuff, but wanted this functionality in atleast now so once we go ahead and clean everything up once we stabilise, main things are in.

🔍 Related Issues

Closes #262

[gemini-code-assist]

Summary of Changes

Hello @SequeI, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request introduces a new manage subcommand under the agentup plugin CLI, enabling users to add or remove capability scopes for specific plugins within the agentup.yml configuration file. This enhancement provides granular control over plugin permissions directly from the command line, supporting features like dry-runs and explicit configuration file targeting.

Highlights

• New plugin manage Command: A new CLI command agentup plugin manage is introduced, allowing users to modify plugin capability scopes.
• Scope Management Options: Users can add scopes using -a/--add-scope <capability_id>::<scope> and remove scopes using -r/--remove-scope <capability_id>::<scope>. Both options are repeatable.
• Mutual Exclusivity: The --add-scope and --remove-scope options are mutually exclusive, preventing conflicting operations in a single command. This is enforced by a new MutuallyExclusiveOption class.
• Dry-Run Functionality: A --dry-run (-n) flag allows users to preview the planned changes to agentup.yml without actually modifying the file.
• Config File Targeting: The --config <path> option enables specifying a custom path for the agentup.yml file, overriding the default location.
• Enhanced User Feedback: The command provides clear messages for successful operations, existing scopes, missing scopes, invalid formats, and unknown plugins/capabilities.

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[gemini-code-assist]

Code Review

This pull request introduces a new plugin manage command to add and remove capability scopes, along with a reusable MutuallyExclusiveOption for click commands. The implementation is solid and includes a comprehensive set of tests.

My feedback focuses on improving user experience with clearer error messages and help texts, enhancing robustness by handling error conditions more gracefully (e.g., exiting with a non-zero status code on error), and increasing code clarity through some minor refactoring and simplification. These changes will make the new command more reliable and easier to maintain.

[SequeI]

Need to solve some bugs here

[SequeI]

Solved, ready. Had a weird edgecase.