Refactor documentation structure and remove legacy files

[fajarhide]

PR Auto Describe

Summary

This PR overhauls OMNI's documentation ecosystem, consolidating all user-facing guides into a single comprehensive docs/HOW_TO_USE.md, removing redundant standalone files, and updating top-level and security documentation to reflect v0.5.x platform changes including updated trust logic and SQLite-backed metrics storage.

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Key Changes

1. Full documentation consolidation: Merged all install, CLI, filter, and learning guides into one centralized user guide
2. Removed 4 deprecated standalone documentation files
3. Updated README.md with a new structured documentation index
4. Revised SECURITY.md to match current v0.5.x functionality and reporting processes

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Detailed Breakdown

File Modifications

• Deleted: Root INSTALL.md, docs/CLI_REFERENCE.md, docs/FILTERS.md, docs/LEARN.md (all content migrated to docs/HOW_TO_USE.md)
• Added: 1,100+ page docs/HOW_TO_USE.md covering installation, daily usage, RewindStore, session tracking, custom filters, troubleshooting, and setup checklists

Top-level Documentation Updates

• README.md: Added a new Documentation Index section splitting user/developer resources, linked all core project docs, and updated custom filter references
• SECURITY.md:
  • Updated supported version matrix to mark v0.5.x as active, v0.4.x as deprecated
  • Revised vulnerability reporting to prioritize GitHub Issues
  • Updated trust logic to include project-local .omni/filters/ directories alongside omni_config.json
  • Swapped metrics storage from CSV to local SQLite database (~/.omni/omni.db)
  • Trimmed and updated the list of sanitized environment variables
  • Renamed all references to the legacy omni_trust MCP tool to match the current omni trust CLI command

Alignment

• All documentation now matches the current v0.5.x CLI behavior and project architecture

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Notes

Existing users relying on the deprecated omni_trust tool name will need to update their automations to use omni trust instead.

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Breaking Changes

1. The MCP tool previously named omni_trust is now omni trust, breaking any existing automations that call the old tool name
2. Historical CSV metrics data will not be automatically migrated to the new SQLite database, so omni stats will not show pre-upgrade stats
3. Project-local filters now require explicit trust via omni trust instead of loading automatically, which may break existing project filter setups

Last updated: 2026-04-09 08:25:11