On the Projects tab, there are two directories that define your project: Project Path and Source Directory. The project path should always point to the "root" directory containing the "project.xdk" file (it represents the top level of your project). The Source Directory can point to a subdirectory in the project that contains only those files that are related to the assembly (it should contain the "source" files that actually represent your project).
" ", " " - , . * wild card . , (.git,.GIT,.svn,.SVN,.cvs,.hg,.HG,.CVS,.ignore,.IGNORE,.DS_Store) . , , .hg . , , , , - *.py.