fix: add cross-file Ref declarations for relspecgo merge

- Add explicit Ref: blocks at bottom of each DBML file for cross-file FK relationships
- files.dbml: stored_files → thoughts, projects
- skills.dbml: project_skills/project_guardrails → projects
- meta.dbml: chat_histories → projects
- Update Makefile to use the relspec merge workflow where applicable
- Regenerate 020_generated_schema.sql with proper cross-file constraints

Addresses review comment on PR #20

schema/files.dbml

@@ -19,3 +19,7 @@ Table stored_files {
     sha256
   }
 }
+
+// Cross-file refs (for relspecgo merge)
+Ref: stored_files.thought_id > thoughts.guid [delete: set null]
+Ref: stored_files.project_id > projects.guid [delete: set null]