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pixel install deploys a second, short (under 2 KB) prompt to ~/.local/share/pixel/subagent-prompt.md and the claude shell wrapper passes it with --append-subagent-system-prompt-file whenever -p/--print is among the arguments (bash, zsh and fish). Claude Code sub-agents receive neither the session's --append-system-prompt-file nor its history, and honour the sub-agent flag in print mode only. The flag is written only when claude --version reports 2.1.261 or newer (the release that added it; older ones exit 1 on the unknown option): below that, install writes the plain wrapper and reports the step yellow with the version found; with no usable claude (not on PATH, no answer within 5 s, unparseable version) it keeps the flag decision of the existing block, or writes the plain wrapper on a first install, and reports yellow. A short-flag cluster containing p (-pc, -cp) counts as print mode. pixel doctor gains an install.subagent-prompt check, re-derives the expected wrapper from the Claude Code found at check time (red in both directions: flag in front of an old Claude Code, or missing in front of a new one; yellow when claude cannot be probed), and pixel uninstall removes the file. The task-worker command builder accepts a matching subagent_prompt_file option; nothing sets it yet.
Fixed
The bundled agent prompt (agent-prompt.md) no longer documents command lines the CLI rejects: pixel uses "X" --callers|--callees is --role callers|callees, publish/ship/branch/update take --request-id (there is no -r), update needs --target-oid and --expected-head, lifecycle takes --file <path>, sync needs a remote. The "installed at ~/.local/bin/pixel" sentence, wrong for mise/Homebrew/CI installs, now points at command -v pixel.
pixel publish --files <path> (and ship) no longer fails with git add: pathspec '<path>' did not match any files when <path> is a deletion already staged with git rm. Paths absent from both the worktree and the index skip the git add step and are committed by the pathspec-scoped git commit; a path git has never known is still rejected, and no commit is created.