docs: add internal subsystems and plugin slash commands reference

[akshatmalik-bruh]

Summary

• Documented Core Runtime Subsystems: Added detailed architectural and reference documentation for BLAS thread pool pre-allocation limits (core/blas_threads.py), inter-process update locking & coordination (core/update_lock.py), and HMAC cache security sealing against CWE-502 (core/cache_seal.py).
• Documented Missing Environment Variables: Added entries to CONFIG.md for REPOWISE_NO_SAVE_KEY, REPOWISE_MCP_NO_WATCHDOG, REPOWISE_INDEX_INFORMATION_FLOOR, BLAS thread control variables (OPENBLAS_NUM_THREADS, MKL_NUM_THREADS, NUMEXPR_NUM_THREADS, VECLIB_MAXIMUM_THREADS), and HMAC cache key overrides (REPOWISE_CACHE_HMAC_KEY, REPOWISE_CACHE_KEY_PATH).
• Added Plugin Slash Commands Reference: Created docs/agent/CLAUDE_CODE_COMMANDS.md providing complete reference documentation for all 18 /repowise:* slash commands included with the Claude Code plugin, and cross-linked it from INTEGRATIONS.md.

Related Issues

• Addresses documentation audit findings for internal engine subsystems, hidden environment variables, and agent integration commands.
• fixes [Docs] Add documentation for BLAS thread pool limits, update locking, HMAC cache security, and plugin slash commands #2089

Test Plan

• Markdown syntax and link integrity verified across modified files (CONFIG.md, AUTO_SYNC.md, ARCHITECTURE.md, INTEGRATIONS.md, CLAUDE_CODE_COMMANDS.md).
• Verified cross-file links between INTEGRATIONS.md and CLAUDE_CODE_COMMANDS.md.

Checklist

• My code follows the project's code style
• I have added tests for new functionality (N/A — documentation only)
• All existing tests still pass
• I have updated documentation if needed