Same directory tree for annotations, invalid chars in library names fix

- implemented an option to output all annotation results to the same directory tree (instead of creating a separate subtree for each library in the output directory).

Now when picking a library with the following symbols in its name (defined in project properties):
  \/:*?\"<>|
  AND putting every library's annotation into separate directory subtrees, we will replace these symbols for underscores in names of directories, containing subtrees.
  The reason is that these characters are not allowed as parts of filenames (i.e. in Windows).
Merge remote-tracking branch 'upstream/master'
moved checkbox "Use common directory tree"  below the "Output folder" input field