Disclose backend hardening and route changes

From the PR description

Part of the downstream AGPL disclosure. This PR isolates backend hardening and route changes for easier review.

Scope

• Backend source changes for app bootstrapping, auth-aware APIs, storage, uploads, LLM routing, chat tools, account lifecycle, logging, and validation.
• Full disclosure PR: #127.

App and Configuration

• Adds backend/src/app.ts to separate Express app construction from server startup.
• Adds typed environment handling in backend/src/env.ts.
• Updates backend package dependencies, scripts, lockfiles, TypeScript settings, and deployment config.

Auth, Access, and User Lifecycle

• Hardens auth middleware and Supabase access helpers.
• Adds encrypted user model key handling through user settings and model routes.
• Adds account deletion, restore token, and deletion worker support.
• Adds validation helpers used by route inputs.

Chat, LLM, and Tools

• Splits the previous large chat tools module into focused modules under backend/src/lib/chatTools/.
• Adds structured tool schemas, tool runner behavior, document context loading, citation handling, workflow store helpers, streaming support, and individual tools.
• Updates Anthropic and Gemini integration behavior and removes the old OpenAI-specific module path.
• Adds model availability routing through a backend models endpoint.

Storage, Uploads, and Documents

• Updates storage, upload, download token, and document route behavior.
• Adds PDF queue and structure tree helpers.
• Improves document upload, project document, tabular, workflow, and download API behavior.

Operations and Safety

• Adds Pino request logging support.
• Adds LLM request rate limiting.
• Adds helper code for restore tokens, crypto, and safer route validation.

Review Note

• Database schema support for some backend behavior is disclosed in #130. Frontend flows that call these endpoints are disclosed in #128. Test coverage for this behavior is disclosed in #129.