Add comprehensive file-level DOX documentation across the repo and update directory AGENTS.md indexes. Many new `*.py.dox.md` files were added under api, helpers, tools, plugins, extensions, webui, and other dirs to document endpoint purpose, ownership, runtime contracts, work guidance, and verification. Several AGENTS.md files were created or updated (agents profiles, api, docker, extensions, helpers, plugins, skills, webui components, etc.) to list child DOX files and clarify documentation/work guidance. Also add example and bundled profile DOX files (agent0, default, developer, hacker, researcher) and minor updates to helpers/dirty_json.py and its tests. These changes improve on-disk documentation coverage and establish the convention that each direct runtime file should have a matching `*.dox.md` describing its contracts and verification steps.
- Refactor API key management: move from global env-only to per-model config with dotenv fallback
- Add API key placeholder masking and reveal functionality in WebUI
- Consolidate API key validation logic into `has_provider_api_key()` helper
- Improve update system: add branch filtering for tags, simplify backup naming
- Add branch detection to version info and default to current branch for updates
- Extract configure model settings link to constant
- Move allow_chat_override from chat_model to top-level configuration
- Update all references to use new config path
- Set default to true in default_config.yaml, false in migration
- Fix datetime parsing to handle timezone-less ISO strings by appending 'Z'
- Remove inline style from tune icon in config.html
