DefaultStartTimeout (30s) too short for large knowledge bases (#4060 follow-up)

[aheritier]

Context

The #4060 remediation plan authorized raising DefaultStartTimeout from 30 s to a value generous enough for large RAG knowledge bases. PR #4062 explicitly deferred this.

Problem

DefaultStartTimeout = 30s (pkg/tools/startable.go) aborts RAG initialization runs after 30 s, discarding all partial indexing work and triggering a re-index from scratch on the next turn.

Acceptance criteria

• DefaultStartTimeout raised (or made configurable per-toolset) so large knowledge bases complete indexing without being aborted
• Per-file indexing progress persisted so a timeout does not discard already-indexed files