Update Agent Permissions

# Task: Update Agent Permissions

Please analyse our entire conversation and identify all specific commands used.

Update permissions for both Claude Code and Gemini CLI.

## Reference Files

- Claude: ~/.claude/settings.json
- Gemini policy: ~/.gemini/policies/tool-permissions.toml
- Gemini settings: ~/.gemini/settings.json
- Gemini trusted folders: ~/.gemini/trustedFolders.json

## Instructions

1. Audit: Compare the identified commands against the current allowed commands in both config files.
2. Filter: Only include commands that provide read-only access to resources.
3. Restrict: Explicitly exclude any commands capable of modifying, deleting, or destroying data.
4. Update: Add only the missing read-only commands to both config files.
5. Constraint: Do not use wildcards. Each command must be listed individually for granular security.

Show me the list of commands under two categories: Read-Only, and Write

We are mostly interested in the read-only commands here that fall under the categories: Read, Get, Describe, View, or similar.

Once I have approved the list, update both config files.

## Claude Format

File: ~/.claude/settings.json

Claude uses a JSON permissions object with allow, deny, and ask arrays.

Allow format: `Bash(command subcommand:*)`

Insert new commands in alphabetical order within the allow array.

## Gemini Format

File: ~/.gemini/policies/tool-permissions.toml

Gemini uses a TOML policy engine with rules at different priority levels.

Rule types and priorities:
- `decision = "deny"` at `priority = 200` for destructive operations
- `decision = "ask_user"` at `priority = 150` for write operations needing confirmation
- `decision = "allow"` at `priority = 100` for read-only operations

For allow rules, use `commandPrefix` (provides word-boundary matching).
For deny and ask rules, use `commandRegex` (catches flag variants).

New read-only commands should be added to the appropriate existing `[[rule]]` block by category, or a new block if no category fits.

Example allow rule:
```toml
[[rule]]
toolName = "run_shell_command"
commandPrefix = ["command subcommand1", "command subcommand2"]
decision = "allow"
priority = 100
```

## Gemini Directories

If any new directories outside the workspace were accessed, add them to:
- `context.includeDirectories` in ~/.gemini/settings.json
- ~/.gemini/trustedFolders.json with value `"TRUST_FOLDER"`

## Exceptions

Do not suggest adding the following commands:

- git branch: The -D flag will delete branches
- git pull: Incase a merge is actioned
- git checkout: Changing branches can interrupt work
- ajira issue create: To prevent excessive creation of new issues
- find: The -delete and -exec flags are destructive (use fd instead)