chore: persist memories and excerpts under knowledge/ instead of .claude/

Move documented and skill paths to knowledge/memories and knowledge/files
(project root, mappable to @knowledge) to reduce sandbox issues on .claude/.
Update CLAUDE.md memory protocol, update-mykb-* skills, and settings.local.json
bootstrap check for core.json.

Made-with: Cursor

.gitignore

@@ -5,6 +5,7 @@ __pycache__/
 dist/
 build/
 workspace/
+knowledge/
 
 .claude/
 .obsidian/