[Architecture][P1] Phase 1: Extract reusable bootstrap and unify server routes

Parent: https://github.com/terraphim/terraphim-ai/issues/520
Related plan: docs/architecture-improvement-plan.md

Goal

Extract reusable startup boundaries in the server layer so composition roots stay thin and test/prod router behavior stays in sync.

Deliverables

• Reusable runtime bootstrap module/crate for rolegraph + indexing initialization
• Shared route composition function used by both production and test router constructors
• Thin composition-root entrypoints in terraphim_server/src/main.rs and terraphim_server/src/lib.rs

Tasks

• Extract startup indexing logic from terraphim_server/src/lib.rs into a reusable initializer component
• Replace duplicated route lists with a single route composition function
• Add focused tests to verify production/test router parity
• Document the new boundary in module/crate README or ADR references

Acceptance Criteria

• No duplicated route registration blocks across production/test constructors
• Startup/indexing orchestration can be reused from tests or other adapters
• Build/test paths pass for server with default and relevant feature sets

Start with terraphim_server/src/lib.rs and terraphim_server/src/main.rs, then read docs/architecture-improvement-plan.md and the parent issue for the intended boundaries. Trace the startup indexing logic and the production/test route constructors before deciding how to extract them. Done means shared route registration, reusable startup orchestration, focused parity tests, documentation, and passing server builds/tests across relevant feature sets.