…aset

The computation previously needed to read the SpimData and went through
all the SpatialTemporalIndex. This can be simplified to one iteration
over the list of spots which is actually a lot less complex than creating
the SpatialTemporalIndex.

Change exception handling. Exception are handled by the caller.
Change method ignorePattern() to relevantFilesFilter().
Simplify isClean

MastodonGitUtils -> MastodonGitRepository
MastodonGitPlugins -> MastodonGitController

…ubdir

…lable

This is necessary to have a complete up to date list of remote branches.

It is very easy to initialize a repository when using github or gitlab.
And is impossible to go back to the uninitialized state. So it is better
for the "share project" command to assume that the github / gitlab repo
was already created. That way we also don't need to decide whether to
call the default branch "main" or "master".

Previously the reset command would fail. If for example the user made
some changes, and then saved them to disc.

…ible

Why is this necessary? I don't now. But "extends Service" would lead to
a missing service error when starting Mastodon from within Fiji.

Co-authored-by: Stefan Hahmann <[email protected]>

Try to improve code readability by introducing a callback method for
the interaction between the SingleUseCredentialsProvider and the
PersistentCredentials class.

Improve thread safety by making the getUsernameAndPassword method
syncronized. This avoids to show multiple dialogues in parallel to
the user in parallel.

… better

Previously: The user clicking cancel on the username & password dialog
inderectly triggered a TransportException. The exception message would
be shown in an error dialog, and the stack trace was printed on the
console.

Now: The user clicking cancel throws a CancellationExcpetion. The
exception is catched at an appropriate location and no confusing
error dialog or stack trace is shown.

Avoid to print stack traces on the console.

Don't throw the very generic RuntimeException

Move the demo code into the src/test/java folder.
Make sure the dialogues are properly disposed such that they can be garbage
collected and that the JVM properly shuts down.

Users will see the command identifiers in the short-cuts config page.
These identifiers should therefor be understandable.

The class is replace with the CommitMessageDialog