chore: mark INCREMENTAL-GRAPH proposal/plan completed, bump to v0.4.0 (#286)

Move INCREMENTAL-GRAPH-PROPOSE.md and PLAN-INCREMENTAL-GRAPH.md to completed directories. Bump version to 0.4.0 and publish to PyPI.

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

Author: HumanBean17

plans/active/PLAN-INCREMENTAL-GRAPH.md plans/completed/PLAN-INCREMENTAL-GRAPH.mdplans/active/PLAN-INCREMENTAL-GRAPH.md renamed to plans/completed/PLAN-INCREMENTAL-GRAPH.md

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "java-codebase-rag"
-version = "0.3.1"
+version = "0.4.0"
 description = "MCP server for semantic + structural search over Java codebases"
 readme = "README.md"
 requires-python = ">=3.11"