Configuration

jgo is configured through a combination of settings files, environment variables, command-line flags, and jgo.toml project files.

Settings file

The global settings file uses INI format. jgo checks these locations in order:

~/.config/jgo.conf (XDG Base Directory standard – recommended)
~/.jgorc (legacy location, still supported)

If both exist, the XDG location takes precedence.

Format

[settings]
cacheDir = ~/.cache/jgo
m2Repo = ~/.m2/repository
links = hard

[repositories]
scijava.public = https://maven.scijava.org/content/groups/public

[shortcuts]
imagej = net.imagej:imagej
fiji = sc.fiji:fiji:LATEST
jython = org.python:jython-standalone
repl = imagej:org.scijava.script.ScriptREPL

`[settings]` section

cacheDir: Root directory for cached environments. Default: ~/.cache/jgo.
m2Repo: Local Maven repository cache. Default: ~/.m2/repository.
links: Link strategy for JARs: hard, soft, copy, or auto. Default: hard.

`[repositories]` section

Additional remote Maven repositories. Maven Central is always included. Each entry is name = URL:

[repositories]
scijava.public = https://maven.scijava.org/content/groups/public
myrepo = https://repo.example.com/maven2

You can also pass repositories on the command line with -r:

jgo -r scijava=https://maven.scijava.org/content/groups/public org.scijava:parsington

Tip

For more control over Maven repository configuration (mirrors, authentication), use Maven’s ~/.m2/settings.xml. See Using Mirrors for Repositories.

`[shortcuts]` section

Shortcuts are aliases that expand to Maven coordinates. They replace the matched prefix at the beginning of an endpoint string:

[shortcuts]
imagej = net.imagej:imagej
fiji = sc.fiji:fiji:LATEST
repl = imagej:org.scijava.script.ScriptREPL

Usage:

jgo imagej              # Expands to: net.imagej:imagej
jgo imagej:2.15.0       # Expands to: net.imagej:imagej:2.15.0
jgo repl                # Expands to: net.imagej:imagej with main class
jgo repl+groovy         # Combines multiple shortcuts

Shortcut rules:

Shortcuts match at the start of a coordinate (or each +-separated part).
Anything after the matched name is preserved (e.g., imagej:2.0.0 keeps :2.0.0).
Shortcuts can reference other shortcuts and are expanded recursively.
Composition with + treats each part independently.

Managing shortcuts from the CLI:

jgo config shortcut                          # List all shortcuts
jgo config shortcut imagej                   # Show expansion
jgo config shortcut imagej net.imagej:imagej # Add/update
jgo config shortcut --remove imagej          # Remove

Environment variables

Variable	Description	Equivalent flag
`JGO_CACHE_DIR`	Override cache directory	`--cache-dir`
`M2_REPO`	Override Maven repository location	`--repo-cache`
`JAVA_HOME`	Java installation (when using system Java)	`--system-java`
`JAVA_VERSION`	Force specific Java version	`--java-version`
`JGO_OFFLINE`	Work offline	`--offline`
`JGO_UPDATE`	Update cached environment	`--update`
`JGO_NO_CACHE`	Skip cache	`--no-cache`
`JGO_LENIENT`	Warn instead of fail on unresolved deps	`--lenient`
`JGO_INCLUDE_OPTIONAL`	Include optional dependencies	`--include-optional`
`COLOR`	Output color mode	`--color`

Precedence

Configuration is merged with this precedence (highest to lowest):

Command-line flags (--cache-dir, -r, etc.)
Environment variables (JGO_CACHE_DIR, etc.)
jgo.toml settings (in project mode)
Settings file (~/.config/jgo.conf or ~/.jgorc)
Built-in defaults