docs: overhaul docs, trim AGENTS.md, expand BRANCHING.md, rewrite SECURITY.md

[aadil96]

Summary

• AGENTS.md: Trimmed from 150→74 lines. Moved git safety rules to BRANCHING.md. Used concise tables.
• BRANCHING.md: Expanded with pre-change verification, safe ops whitelist, ask-before-doing list, rationale.
• SECURITY.md: Replaced generic template with repo-specific policy (scope, key rules, deps, CI, reporting).
• quality-gates.md: Updated for dotfiles context — ShellCheck + markdownlint gates.
• troubleshooting.md: Added 7 entries (chezmoi init, mise, Brewfile, Tailscale, ShellCheck, markdownlint, externals, dev container).
• opencode.json: Relaxed permission model, kept protected-branch guards.
• Cleanup: Removed 4 empty doc stubs.

Review

Reviewed via code-review skill. Only findings were opencode.json permissions (user approved).

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[what-the-diff]

PR Summary

• Enhanced .chezmoi.toml.tmpl support and scripting

  • Added a new environment variable DEVPOD to detect remote environments.
  • Enabled non-interactive scripting for collecting configuration values from environment variables, thereby improving automation.
  • Incorporated tailscale_authkey configuration variable for Tailscale integration.

• Script additions and removal

  • Created a script to install and authenticate Tailscale.
  • Removed an obsolete script related to the aeos installation.
  • Introduced a new script for handling Homebrew bundle installations.

• Settings and documentation improvements

  • Added a JSON settings file for managing permissions.
  • Updated documentation for clarity, highlighting quick commands, repo structure, enhanced security, practices around handling secrets and CI, and better error handling.

• Homebrew and Shell updates

  • Added HOMEBREW_BUNDLE_FILE in .bashrc for consistent access to Brewfile.
  • Introduced a new Brewfile to manage Homebrew packages.
  • Updated dependencies, including new packages and version updates.

• Plugin and Configuration enhancements

  • Updated, added, and modified plugins and their dependencies in lazy-lock.json.
  • Enhanced extras configuration with the addition of new plugins in lazyvim.json.
  • Refined Zsh configuration with added functionalities like completion support and a new function.

• Permissions and Setup script improvements

  • Modified permissions settings for various commands, ensuring better control over critical commands.
  • Improved the setup script by adding checks, enhancing the configuration mode, and correctly structuring the ChezMoi application command for applying dotfiles.