Initialize DeepOrbit

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 99System/DeepOrbit/skills/, writes 99System/DeepOrbit/skills-index.json, overlays missing system templates/prompts/Bases, refreshes mentor guides, and copies a curated runtime bundle into 99System/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, nodemodules, 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:

1. Read the JSON result.
2. If conflicts is non-empty, show every path and ask the user how to merge it; do not delete either file.
3. Run deeporbit --vault "<vault-path>" doctor.
4. Explain which optional capabilities are available. Missing Obsidian CLI, ChromaDB, Tasks, Dataview, or Calendar must not be treated as initialization failures.