docs(docs): clean up implementation leaks, reorganize memory index, and expand synapse submodules

[sbharatjoshi]

Summary of Changes

This Pull Request reorganizes the Spector OSS documentation in the core repository, cleans up leaked Java implementation details, substantially expands the synapse agentic documentation layer, and introduces theme-aware Mermaid styling.

1. Reorganized & Cleaned Up Cognitive Memory Docs

• docs/docs/memory/index.md: Reordered the flagship Cognitive Memory landing page (Vision & Philosophy → 4-Tier Functional Model → Biological Metaphors → Advantages & Benchmarks → Deep Dives). Removed Java-specific references like Arena.ofShared() and FileChannel.map() from high-level summaries.
• docs/docs/memory/cortex.md: Replaced technical details like FileChannel and mmap with functional/high-level descriptions.
• docs/docs/memory/architecture.md: Standardized Custom Tier descriptions.

2. Expanded Synapse & Agentic Layer Documentation

• docs/docs/synapse/index.md:
  • Removed AgentSoul class-level fields and UML class diagrams.
  • Documented the relationship between the Agent Soul (personality/governor) and the User Salience Profile (personalized retrieval filter) and how they complement each other.
  • Added functional descriptions and sequence/flow charts for submodules: Agentic Chat Graph, Dynamic Agent Execution (FlowSpec compiler), Memory Bridge, LLM Provider Registry, Data Connectors, and the Plugin System.
  • Added new operational sections for Observability & Tracing (thought/action/observation inspection), Failure Recovery & Loop Prevention, and Workflows vs. Autonomous Agents.

3. Theme-Aware Mermaid Styling

• docs/docs/stylesheets/extra.css: Appended CSS class definitions matching Material theme variables for both slate (dark) and default (light) schemes.
• Mapped all modified Mermaid diagrams to these new classes (e.g., :::working, :::episodic, :::synapse, :::cortex), removing all hardcoded style attributes.

Verification

• Verified by compiling with mkdocs build, which succeeded in 2.84s with zero warnings/errors on modified files.
• Verified local rendering by serving the site in the background.