It seems that the new version does not handle symbolic links in the path of the Bisq application directory the same way anymore.
I could reproduce the behavior in first moving away the application directory and then creating a symbolic link at its place:
$ mkdir ~/tmp
$ mv ~/.local/share/Bisq/ ~/tmp
$ ln -s ~/tmp/Bisq/ ~/.local/share/Bisq
$ ./gradlew :desktop:run
> Task :desktop:run FAILED
fault: An unexpected error occurred. Please file a report at https://bisq.network/issues
java.io.UncheckedIOException: Application data directory '/home/xxx/.local/share/Bisq' could not be created
at bisq.common.config.Config.mkAppDataDir(Config.java:805)
at bisq.common.config.Config.<init>(Config.java:644)
at bisq.core.app.BisqExecutable.execute(BisqExecutable.java:76)
at bisq.desktop.app.BisqAppMain.main(BisqAppMain.java:57)
Caused by: java.nio.file.FileAlreadyExistsException: /home/xxx/.local/share/Bisq
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:94)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116)
at java.base/sun.nio.fs.UnixFileSystemProvider.createDirectory(UnixFileSystemProvider.java:385)
at java.base/java.nio.file.Files.createDirectory(Files.java:689)
at java.base/java.nio.file.Files.createAndCheckIsDirectory(Files.java:796)
at java.base/java.nio.file.Files.createDirectories(Files.java:742)
at bisq.common.config.Config.mkAppDataDir(Config.java:803)
... 3 more