$ contree run --helpusage: contree run [-h] [-t TIMEOUT] [-C CWD] [-e ENV] [-H HOSTNAME] [-D] [-I] [-s] [-F FILE] [--file-excludes PATTERN [PATTERN ...]] [-T TRUNCATE] [--preserve-env] [-d] [--use IMAGE] ...Spawn a sandbox instance from the current session image and execute a command.Uses the image from the active session (set via `contree use IMAGE`),or an image specified inline via ``--use IMAGE``.Commands are passed after -- separator; without --, the firstpositional arg is the command.By default the CLI polls until the operation reaches a terminalstatus (SUCCESS, FAILED, CANCELLED) and prints stdout/stderr.Use -d/--detach to exit immediately after spawning.File attachments: Use --file to inject host files or directories into the sandbox before execution. Files are uploaded to the API (with SHA256 dedup) and mounted at the specified instance path. Ownership and permissions default to host file stat unless overridden. Note: non-disposable runs persist filesystem changes into a new image. Files attached once are already part of that image and do not need re-attachment. Use --disposable to discard changes after execution. Format: host_path[:instance_path][:uUID][:gGID][:mMODE] host_path all defaults from stat host_path:/inst/path point a destination path host_path:m0755 override only mode host_path:/inst/path:u0:g0:m0755 all explicit host_path:uroot:groot uid/gid by name (local) Tagged options (u/g/m) can appear in any order after host_path. instance_path is detected by its leading /. For directory attachments, files are walked recursively and default excludes are applied: .*, .git, *.pyc, __pycache__, .venv, .mypy_cache, .pytest_cache, node_modules, dist, build. Add extra patterns with --file-excludes. The CLI also keeps a local upload cache keyed by path+inode+mtime+size and reuses known file UUIDs to avoid unnecessary re-upload checks/uploads. Note: named uid/gid (e.g. uroot) are resolved locally via pwd/grp — use numeric IDs if unsure about host/sandbox mismatch.positional arguments: command_args Command and arguments (after --)options: -h, --help show this help message and exit -t TIMEOUT, --timeout TIMEOUT Timeout in seconds (default: 120) -C CWD, --cwd CWD Working directory inside sandbox, absolute path or empty string for use sandbox WORKDIR (default: ) -e ENV, --env ENV Environment variable KEY=VALUE (repeatable) -H HOSTNAME, --hostname HOSTNAME Container hostname (default: linuxkit) -D, --disposable Drop filesystem changes after run -I, --interpreter Interpreter (shebang) mode. Read the script file given as the first argument, strip the #! line, and send the body as stdin to /bin/sh -s. Usage: #!/usr/bin/env -S contree run -I -s, --shell Join command args into a single shell expression -F FILE, --file FILE Attach file or directory (repeatable, dirs recurse). Format: host[:inst_path][:uUID][:gGID][:mMODE]. Tagged options (u/g/m) in any order; uid/gid resolved locally from pwd/grp; defaults from host stat. --file-excludes PATTERN [PATTERN ...] Additional glob exclude patterns for directory attachments (repeatable). -T TRUNCATE, --truncate TRUNCATE Truncate output to N bytes (default: 65536) --preserve-env Preserve env vars from previous run (server-side) -d, --detach, --no-wait Exit immediately after spawning (do not wait for result) --use IMAGE Switch session to IMAGE before running (UUID or tag:NAME). Equivalent to 'contree use IMAGE' followed by 'run'. Recorded in session history and can be rolled back with 'session rollback'. (default: )examples: contree use ubuntu && contree run -- uname -a contree run --use tag:ubuntu:latest -- uname -a contree run --shell -- 'echo hello && ls /' contree run -e FOO=bar DEBUG=1 -- ./app contree run --file ./app.py:/app.py --disposable -- python /app.py contree run --file ./src:/app/src --file-excludes '*.log' -- make -C /app/src contree run -d -- sleep 3600for coding agents: `run` executes remotely inside the instance image (not on local host) local files/dirs must be mapped with --file to be available remotely mutates session image unless --disposable is set supports directory attachments via --file host_dir:/instance_dir local file cache avoids re-upload when path+inode+mtime+size unchanged returns command exit code when available default formatter prints raw stdout/stderr only use -f json for structured operation metadataagent note: Before using this command in an automated workflow, read: contree agent