to decompile a jar run following command

./gradlew.bat decompile "-PindexerDecompileInput=<path to jar>" "-PindexerDecompileOutput=<output directory>"

to index JAVA files from source

./gradlew.bat run --args="--source <path to source root> --output <output directory> --pretty <true or false>"

to index JAVA from dependency

./gradlew.bat indexDependency "-PindexerDependency=<group:artifact:version>" "-PindexerOutput=<output directory>" "-PindexerTransitive=<true or false>" "-Ppretty=<true or false>"