Files ctrlyoke writes

To detect when a step finishes, attach MCP servers, apply tool permissions and report usage, ctrlyoke has to configure each harness CLI. Where a CLI accepts configuration on the command line or through environment variables, ctrlyoke passes it that way and writes nothing. Where a CLI only reads configuration from disk, ctrlyoke writes the smallest file it can, tracks exactly what it added, and removes it again.

This page lists every file, per harness, so that nothing in git status or your home folder comes as a surprise.

Every harness: .ctrlyoke/temp/

Each run writes working files into the workspace's .ctrlyoke/temp/ folder: prompt files, generated MCP configuration, per-prompt hook settings, the signal files hook scripts write when a step ends (<cli>-notifications/), and status line snapshots. The generated .ctrlyoke/.gitignore ignores temp/, so none of it shows in git status.

Files are deleted when the prompt or run that used them finishes. When VS Code starts, ctrlyoke also deletes anything left in .ctrlyoke/temp/ that is more than 24 hours old, which covers runs that were killed before they could clean up.

Every harness with a status line: global settings

Claude Code, Copilot, Qwen Code and Antigravity can show a status line in their own terminal UI, and Claude Code and Antigravity report their quota only through it. To read it, ctrlyoke points that harness's global status line setting at a small script it keeps in ~/.ctrlyoke/bin/:

Harness	File	Key
Claude Code	~/.claude/settings.json	statusLine
Copilot	~/.copilot/settings.json	statusLine
Qwen Code	~/.qwen/settings.json	ui.statusLine
Antigravity	~/.gemini/antigravity-cli/settings.json	statusLine

Unlike everything else on this page, this is a lasting change, not a per-run one:

• It is installed the first time ctrlyoke runs that harness, and it stays in place between runs.
• If you already had a status line command, ctrlyoke saves it in its own settings (statusLine.byHarness.<harness>.customCommand) and runs it underneath, so your status line keeps working.
• If your existing status line is not a command, ctrlyoke leaves it alone and turns its own off for that harness.
• To undo it, turn the harness off in Settings → Status Line (or set statusLine.byHarness.<harness>.enabled to false). ctrlyoke then puts your original command back, or removes the key if there was none. ~/.ctrlyoke/bin/ is removed once no harness and no other ctrlyoke installation uses it.
• Uninstalling ctrlyoke does the same for every harness once the last ctrlyoke installation is gone. See Uninstall.

Per harness

Copilot CLI

What	Where	Removed
Hooks	.github/hooks/ctrlyoke-<workflow>-p<step>.json	before the next step, and when the run ends
Git ignore file	.github/hooks/.gitignore	once no ctrlyoke hook files remain
MCP servers	.ctrlyoke/temp/, passed with --additional-mcp-config	when the run ends
Context window	.ctrlyoke/temp/ctrlyoke-otel-<workflow>-p<step>.jsonl	when the run ends

Copilot has no command-line option for hooks; it loads every JSON file in the repository's .github/hooks/ folder, so ctrlyoke writes one hook file per step there. To keep those files out of git status, it also writes a .gitignore in that folder that ignores ctrlyoke-*.json and itself, but only if the folder has no .gitignore of its own. Your own .gitignore is never edited.

The OpenTelemetry file is how ctrlyoke reads Copilot's live context-window size. ctrlyoke sets COPILOT_OTEL_FILE_EXPORTER_PATH for each Copilot process it starts, which also overrides any value you have set globally.

Claude Code

What	Where	Removed
Hooks	.ctrlyoke/temp/claude-hook-settings-<workflow>-p<step>.json, passed with --settings	when the run ends
MCP servers	.ctrlyoke/temp/mcp-config-claude-<workflow>.json, passed with --mcp-config	when the run ends

Claude Code layers a --settings file over your own settings for that process only, so ctrlyoke writes nothing outside .ctrlyoke/ in the workspace. When a later step is typed into the same running Claude session (terminal reuse), the hook file is kept until that terminal closes, because Claude rereads it during the session.

Codex CLI

Codex writes nothing to disk. Hooks, the trust entries for those hooks, MCP servers and approval settings are all passed as -c key=value overrides on the command line. ctrlyoke never edits ~/.codex/config.toml or a project .codex/ folder.

OpenCode CLI

Permissions, MCP servers and ctrlyoke's completion plugin are passed to each OpenCode process in the OPENCODE_CONFIG_CONTENT environment variable, and your hooks in another environment variable. To avoid permission-key collisions, ctrlyoke reads OpenCode's global config files, OPENCODE_CONFIG, project opencode.json/opencode.jsonc files from the worktree root through the workspace, their .opencode/ counterparts, and OPENCODE_CONFIG_DIR. It never writes these files or a workspace opencode.json. The plugin is loaded straight from ctrlyoke's install folder.

One fallback writes files: if OpenCode cannot load the plugin from the install folder, ctrlyoke copies it to .opencode/plugin/ctrlyoke-completion-hook.ts (with your hooks in .opencode/plugin/ctrlyoke-hooks.json) and deletes both when the run ends.

Qwen Code

What	Where	Removed
Hooks	.qwen/settings.json, hooks	restored when the last ctrlyoke run in the workspace ends
Hook trust	~/.qwen/trusted_hooks.json	kept on purpose

Qwen reads hooks only from its settings file, so ctrlyoke adds its hooks to the workspace .qwen/settings.json ahead of your own. When the last ctrlyoke run in that workspace finishes, the file's original hooks section is restored. If ctrlyoke created the file, it deletes it, together with a temporary .qwen/.gitignore it writes to hide the file while it exists.

ctrlyoke also marks its own hooks as trusted in ~/.qwen/trusted_hooks.json so that Qwen doesn't ask you to approve them. Those entries stay after the run: removing them would make Qwen ask again next time. Entries you added are never removed.

MCP servers are passed as inline JSON with --mcp-config and are not written anywhere.

Antigravity CLI

What	Where	Removed
MCP servers	.agents/mcp_config.json	when the last ctrlyoke run in the workspace that uses them ends
Hooks	~/.gemini/config/hooks.json	when the run ends

agy has no command-line option for MCP servers; it discovers them from the workspace .agents/mcp_config.json. ctrlyoke adds its servers to that file, keeps any servers that were already there, and removes its own when no running workflow needs them. If ctrlyoke created the file, it deletes it, together with a temporary .agents/.gitignore. On macOS and Linux the file is written readable only by you when a server's env or headers contain a secret. There is no per-prompt server scoping, so workflows running in parallel in one workspace see each other's servers.

agy only reads hooks from the global ~/.gemini/config/hooks.json. ctrlyoke adds one named group per workflow, ctrlyoke-<id>, and removes that group when the run ends. When a later step is typed into the same running agy session (terminal reuse), the group is kept until that terminal closes, because agy rereads the file whenever a hook fires.

Parallel runs

Several workflows can run at once in one workspace, so cleanup never resets a whole file:

• Per-step files are named after the workflow file and the step, so parallel workflows never write the same file.
• For shared files (.qwen/settings.json, .agents/mcp_config.json, ~/.gemini/config/hooks.json, ~/.qwen/trusted_hooks.json), ctrlyoke records which entries belong to which running workflow. A finishing run removes only its own entries. The file's original content comes back only when the last ctrlyoke run using it ends.
• The .github/hooks/.gitignore for Copilot stays while any workflow still has a hook file in that folder.

Why a file can show up in git status

ctrlyoke hides the files it creates, but some changes can still show while a run is active:

• A tracked file was edited. If you commit .qwen/settings.json or .agents/mcp_config.json, it shows as modified during the run and goes back to its committed content afterwards.
• The folder already has your own .gitignore. ctrlyoke doesn't edit a .gitignore it didn't write, so a new file such as .github/hooks/ctrlyoke-*.json shows as untracked until the run ends. Add ctrlyoke-*.json to that .gitignore if this bothers you.
• A run was killed. If VS Code or the CLI is killed mid-run, cleanup can't run. Leftovers are easy to spot by name: delete ctrlyoke-*.json from .github/hooks/, delete ctrlyoke-… groups from ~/.gemini/config/hooks.json, and remove ctrlyoke's hooks from .qwen/settings.json or ctrlyoke's servers from .agents/mcp_config.json. Never commit these files with ctrlyoke's entries in them; they contain absolute paths to this machine.