Run the deterministic initializer from the installed CLI and point it at the DeepOrbit repository checkout that should be materialized into the vault:
deeporbit --vault "<vault-path>" init --source "<deeporbit-repo-path>"
If the deeporbit executable is unavailable, run PYTHONPATH=<repo>/src python -m deeporbit --vault "<vault-path>" init --source "<repo>".
The command is idempotent. It creates missing folders, including 15_Writings, preserves existing notes, merges legacy localized folders only when safe, and reports conflicting files without overwriting either copy.
Initialization materializes the workflow skills into 99_System/DeepOrbit/skills/, writes 99_System/DeepOrbit/skills-index.json, overlays missing system templates/prompts/Bases, refreshes mentor guides, and copies a curated runtime bundle into 99_System/DeepOrbit/repo/. The bundle is the project-level handoff surface: it includes skills, commands, prompts, hooks, CLI source, MCP, docs, and manifests, but excludes .git, virtualenvs, caches, build outputs, node_modules, and generated agent install directories.
External workspaces should install only the global do.link connector; after init, the vault itself carries the workflow catalog needed for routing.
After initialization:
- Read the JSON result.
- If
conflictsis non-empty, show every path and ask the user how to merge it; do not delete either file. - Run
deeporbit --vault "<vault-path>" doctor. - Explain which optional capabilities are available. Missing Obsidian CLI, ChromaDB, Tasks, Dataview, or Calendar must not be treated as initialization failures.