IDE Git Flow, Secrets Panel Improvements, and Bug Fixes

Local git repository support and a guided branch workflow in the IDE:

Auto Initialization — On startup, the backend automatically initializes a local git repository or clones from GIT_REPOSITORY_URL if set, ensuring projects are git-enabled without manual setup
Protected Main Branch — Edits to files on a protected branch are automatically applied to a new branch instead, preventing direct changes to main. Think of it like GitHub Desktop’s branch protection flow
Merge Conflict Resolution — When merging branches, conflicts can be reviewed and resolved directly in the IDE
Branch-Aware File Operations — File and folder create, delete, and rename operations are resolved against the active branch via a branch query parameter on the relevant API endpoints
Git Metadata in Auth Config — The /auth/config endpoint now exposes local_git, git_remote, default_branch, and protected_branches fields for clients to adapt their UI accordingly

Built-in Variables Always Visible — LLM provider API keys (OPENAI_API_KEY, ANTHROPIC_API_KEY, GEMINI_API_KEY) are now always shown in the secrets panel, even before they are referenced in the config or .env file
Improved Variable Discovery — The secrets panel now scans all model key_var fields and database credential variables in the config, ensuring all referenced environment variables are surfaced

Chart Rendering Race Condition — Fixed a race condition in chart rendering where concurrent DuckDB initialization calls could return an uninitialized instance