Closing loop - we merged in a PR that lifted the codex toml modification logic from the codex source code, so it should be safe to use. We weren't able to recreate cases were the previous approach broke our test cases, but by porting codex logic we figure is the best way to structurally ensure there aren't unforseen changes.
I don't believe I've seen a KM app with true WYSWIG that's markdown underneath. Rest is indeed mainly packaging up all the second-brain, MCP, skills, and AI integrations to be out-of-the-box. More to come.
There is a knowledge graph -- we'll update the readme to make clearer. We support wikilinks and forward/backward links are presented to the agent through the MCP server for "agentic search". There's semantic search support as well, etc.
collab between agent <> human happens locally via yjs
collab between human <> human happens using git/GitHub. so collab right now is auto-sync (~few min latency) + sharing functionality. Richer realtime collab is indeed something we're looking at.
If you run into any other issues -- let us know.