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vault: in org.yaml (relative to the org directory; shibaox init writes vault: ../vault, the default org uses ~/.shibaox/vault) points at an Obsidian vault. When a run ends (completed, failed or cancelled), Shibaox writes 10-projects/<project>/runs/<date>-<runId8>.md (status, adapter, spend, nodes, last gate report, timeline) and one 90-system/decisions/<date>-<runId8>-<node>.md per decide node, and prints note: <path>. Notes are never overwritten. Without vault: the run prints one warning.
10-projects/<project>/profile.md is rewritten whenever the project is profiled (the dashboard home, every run). Roles with the memory capability get remember({ scope, text }) and recall({ query }): scope: user appends to 00-org/memory.md, scope: project to 10-projects/<project>/memory.md (dated bullet lines); recall returns the lines containing every word of the query. The last 40 lines of each note (4 kB at most) plus the profile line open every task's prompt, quoted as data.
A code knowledge graph of the project, built with graphify (uv tool install graphifyy; graph build tries this itself when uv is present):
shibaox graph build --project ./project # writes ./project/graphify-out/graph.json
shibaox graph update --project ./project # after code changes
shibaox graph query "where is add defined?" --project ./projectrun --graph auto (the default) uses graphify-out/graph.json when it exists and never builds it: direct roles get a graph_query tool, and Claude Code roles get the graphify MCP server (which needs graphify's Python; a warning is printed and the MCP is skipped when it cannot be found). --graph off disables both.
Once per run, Shibaox matches the org's catalog (org/catalog/*.yaml entries of type skill, plugin, mcp or tool) against the first task role of the workflow and prints autoroute: attach=[...] ambiguous=[...]. Without TYPESAFE_API_KEY the match is by tags; with the key (and a non-mock adapter) Jev scores each candidate and attaches those at 0.8 or more. Today the result gates the graphify MCP: when the catalog lists graphify-mcp, it is attached only if autorouting attaches it.
Events are stored in ~/.shibaox/events.db (SQLite, WAL mode; $SHIBAOX_HOME moves the directory), written only by the daemon. shibaox replay <runId> --db <path> reads a database offline. Deleting the file deletes the run history. Run worktrees live under <project>/.shibaox/worktrees/, run notes in the vault.