| Crate | A loaded collection of containerized commands, identified by namespace/name:tag. |
| Manifest | YAML file defining the commands in a crate, their Docker images, and configuration. |
| Cratefile | Another name for a manifest file. |
| Namespace | Organizational prefix (e.g., databio, bulker). Like a GitHub org. |
| Tag | Version identifier for a crate (e.g., 1.0.13, default). |
| Registry | HTTP endpoint serving manifest YAML files (default: hub.bulker.io). |
| Shimlink | A symlink to the bulker binary. When invoked (e.g., as samtools), bulker checks argv[0] and dispatches to the right container at runtime. |
| Activate | Auto-fetch a manifest, create shimlinks, and put them on your PATH. Works with registry crates and local files. |
| Deactivate | Restore the original PATH, removing crate commands. |
| Exec | Run a single command in a crate’s environment without modifying your shell. |
| Host commands | Native host binaries included in a crate via host_commands in the manifest. In non-strict mode, no shimlink entry is created (they’re found on the preserved PATH). In strict mode, symlinks point directly to the resolved host binary path. |
| Imports | Other crates whose commands are included when a crate is activated. Resolved at runtime. |
| Mock mode | CI/testing mode that replays pre-recorded container outputs without a container runtime. See Mock Mode guide. |
| Engine path | Absolute path to the container engine binary (e.g., /usr/bin/docker), stored in config. Allows the engine to work in strict mode without PATH. |
| Strict mode | Activation mode (-s) where only crate commands are on PATH — no host commands leak through. The container engine still works via its absolute engine_path. |
| Strict-env mode | Activation mode (--strict-env) where containers start with a clean environment. Only variables in the envvars allowlist (config + manifest) are passed. For Docker, limits --env flags. For Apptainer, adds --cleanenv. |
| Auto-mount | Automatic volume mounting triggered by file path arguments. When a shimlinked command receives a non-flag argument that looks like a path, bulker resolves it to an absolute path and mounts its parent directory into the container. No configuration required. |
| Manifest cache | The filesystem directory (~/.config/bulker/manifests/) where fetched manifest YAML files are stored. Acts as the source of truth for installed crates; there is no separate crates map in the config file. |
