Incremental phase execution — detect changes and re-run only affected parts

[nakurian]

Problem

Currently re-running a phase regenerates everything. For example:

• Re-running Phase 3 rewrites ALL specs even if only one service's CONTEXT.md changed
• Re-running Phase 4 regenerates ALL contracts even if only one spec changed

For large projects (10+ services), this wastes time and risks overwriting good specs.

Proposed solution

Add change detection to phases:

1. Track file hashes — maintain phases/.checksums with SHA256 of all input files
2. On re-run — compare current hashes to stored hashes, identify what changed
3. Selective regeneration — only regenerate specs/contracts for affected services
4. Cascade detection — if order-service spec changes, flag contracts that reference it

Example flow:

# User edits services/order-service/CONTEXT.md
/project:3-specify

# Agent detects:
# ✓ web-ui CONTEXT.md unchanged — skipping
# ✓ bff-gateway CONTEXT.md unchanged — skipping  
# ⚡ order-service CONTEXT.md changed — regenerating spec
# → Also flagging: contracts involving order-service may need update

This makes the framework practical for iterative development on large projects.