No possibility to set up paths with the application arguments

UGENE creates an auxiliary folder in some predefined folders and uses a current folder as a working directory (UGENE will write inputs in there, if it executes in the cmdline mod). A possibility to set up paths to folders with the application arguments should be added.

Paths, which are should be set up (almost all of them could be found in the UserApplicationsSettings.h file, some of them in the WorkflowSettings.h file):

1. DownloadDirPath
2. CustomToolsConfigsDirPath
3. RecentlyDownloadedFileNames - no need
4. UserTemporaryDirPath - already done
5. CurrentProcessTemporaryDirPath - no need
6. DefaultDataDirPath
7. FileStorageDir
8. UserDirectory
9. ExternalToolDirectory
10. IncludedElementsDirectory
11. WorkflowOutputDirectory
12. working dir - defined in the WorkflowContext.cpp:191 file