RELEASE: Finalize Semantic Restructuring v0.1.0

- Folders: literate->harness, src->library, system->environment, scripts->interfaces.
- Synchronized all :tangle paths and system definitions.
- Hardened .gitignore for binary and log artifacts.
- Consolidated all documentation into docs/.

Dockerfile

@@ -25,7 +25,7 @@ WORKDIR /app
 COPY . .
 
 # Initialize system in non-interactive mode
-RUN mkdir -p /root/memex && ./opencortex.sh setup --non-interactive
+RUN mkdir -p /root/memex /app/environment/logs && ./opencortex.sh setup --non-interactive
 
 EXPOSE 9105