By default MagicTree checks for orphan project files in tempdir (see Files and Directories) and suggests user to recover or delete them. Command line option --no-crash-recovery disables this behavior, for example:
java -jar MagicTree-onejar.jar --no-crash-recovery
MagicTree uses OneJar software to pack its components into a single JAR file. Most of OneJar's options are described in http://one-jar.sourceforge.net/index.php?page=introduction&file=options, although some of them are undocumented.
Path to mtdir can be overridden (for example to get MagicTree started with "factory" settings) by setting property like following:
java -D one-jar.expand.dir=/tmp/mtdir1234 MagicTree.jar
(If the application was not packed with OneJar, i.e. in development environment, point one-jar.expand.dir.actual property to directory already containing all necessary directories (bin, xslt, ...).
MagicTree keeps user-specific settings in settings.properties file under mtdir. Most of them are updated automatically, but some can be used to customize behavior of the application.
command-monitor-helpers-xtrace: Boolean value. If set to "true', magictree will pass "-x' flag to shell when invoking helpers scripts.