docs: add local embeddings documentation

[nvandessel]

Summary

• New docs/EMBEDDINGS.md: setup guide covering interactive/non-interactive setup, configuration, troubleshooting, and technical details
• Update docs/CLI_REFERENCE.md: add --embeddings / --no-embeddings flags to init command
• Update docs/FLOOP_USAGE.md: add Local Embeddings section explaining the feature and how it works
• Update docs/integrations/mcp-server.md: add note about vector pre-filtering in floop_active
• Update docs/SCIENCE.md: add Embedding-Based Retrieval section covering architecture, model, and lifecycle

Test plan

• All docs are valid markdown
• Cross-references between docs are correct
• No code changes — docs only

🤖 Generated with Claude Code

[greptile-apps]

Greptile Summary

Adds comprehensive documentation for local embeddings feature across five documentation files. The PR introduces docs/EMBEDDINGS.md as a dedicated setup guide and updates existing docs to explain how vector-based semantic retrieval complements the existing predicate matching and spreading activation pipeline.

Key additions:

• New standalone embeddings guide covering interactive/non-interactive setup, configuration via config file and environment variables, troubleshooting, and technical implementation details
• CLI reference updated with --embeddings and --no-embeddings flags for the init command
• Usage guide explains how embeddings work at learn-time and retrieval-time with fallback behavior
• Science doc expanded with embedding-based retrieval architecture, model details, and lifecycle
• MCP server doc notes vector pre-filtering in floop_active tool

Issues found:

• Critical dimension mismatch: documentation states 384 dimensions in multiple locations, but nomic-embed-text-v1.5 produces 768-dimensional embeddings according to the official Nomic AI specification

Confidence Score: 4/5

• Safe to merge after correcting the dimension inconsistency
• Documentation-only PR with clear, comprehensive content and good cross-referencing. Score reduced by 1 point due to a critical technical inaccuracy (384 vs 768 dimensions) that appears in multiple files and affects storage calculations. Once corrected, this will be excellent documentation.
• Pay close attention to docs/EMBEDDINGS.md lines 84, 88, 128 and docs/SCIENCE.md line 139 - all contain the dimension mismatch that needs correction

Important Files Changed

Filename	Overview
docs/CLI_REFERENCE.md	Added --embeddings and --no-embeddings flags to init command with clear examples
docs/EMBEDDINGS.md	New comprehensive guide covering setup, configuration, troubleshooting, and technical details
docs/FLOOP_USAGE.md	Added Local Embeddings section with setup and usage instructions
docs/SCIENCE.md	Added Embedding-Based Retrieval section explaining architecture, model, and lifecycle
docs/integrations/mcp-server.md	Added note about vector pre-filtering in floop_active tool

_{Last reviewed commit: f0ffff8}

[greptile-apps]

_{5 files reviewed, 4 comments}

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