Rename Command Model and separate Shell Gatherer collection - #16
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Rename the project to Command Model and make Shell Gatherer the explicitly separate collection component. The GitHub repository and canonical local repository folder have been renamed with the user's authorization; the old local folder remains a compatibility junction for existing environments and evidence.
Move model source to experiments/command_model and update CI, documentation, agent instructions, new Codex MCP registrations and the integration coordinator's repository identity. Package the unchanged collector as the self-contained skills/shell-gatherer skill; scripts/extract.py remains a forwarding entry point. Mining/labeling/verification stay downstream, and the report becomes shell-analysis.html. Preserve model aliases, frozen partition seeds, historical data directories and unfinished worktrees.
Validation: all 16 required/affected invariant tests passed; Python compilation and skill format validation passed; a separately installed gatherer copy saved 49,822 actual local observations, then the separate analysis pipeline generated and reopened shell-analysis.html and page-data.json. A real Codex CSV handoff used command_model, returned verified results to the frontier, and passed original/alternate-input checks; saved events and summary were reopened. This is rename/integration verification, not a new comparative speed claim. Relative documentation links resolve, all linked worktrees were repaired after the directory move, and unfinished worker changes remain intact. Private transcripts and evidence stay untracked.
Also records Jon's reaffirmed standing agents-merge authorization directly in AGENTS.md, with the shared branch command, isolated worktrees, required coordinator/CI gates and human-only main rule. This fixes the linked-policy ambiguity exposed by the approval rejection; external controls are not bypassed.