repoindex: do not stop indexing when a file could not be indexed

Previously this would create an invalid index

Signed-off-by: Ferry Huberts <ferry.huberts@pelagic.nl>
repoindex: allow directories in the set of files to index

Directories will first be resolved into files, recursively.

Signed-off-by: Ferry Huberts <ferry.huberts@pelagic.nl>
ant: make sure to close the outputstream

Signed-off-by: Ferry Huberts <ferry.huberts@pelagic.nl>
cli: make sure to close the outputstream

Signed-off-by: Ferry Huberts <ferry.huberts@pelagic.nl>