Move configuration options to runtime properties #1799

* generate-debug-attributes
* processing-mode
Simplify preprocessing filter configuration
Clean constant use
Remove old Java command line tool #1800
Use Commons IO #1803
Remove outdated `files.txt` listing for #1804

Fixes #1804
Merge pull request #1805 from infotexture/feature/filelist

Remove outdated `files.txt` listing for #1804
Remove docsrc in favour of separate repo
Add documentation from docs repo
Merge branch 'develop' into feature/store