rebase

Implement 'dump_modify maxfiles' feature

new dihedral table/cut command

Correct small bugs found by static code analysis

Move enums that have to be consistent across files into a class

CMake improvements 

this will trim warnings and error messages when compiling using the CMake
build system, which uses full paths. as a bonus,one can now see, if a
source is taken from a package or not.

- in fix rigid, rigid/small, and poems, a string argument was
  incorrectly assigned to a %d format
- plug two small memory leaks in fix bond/react

Recover jenkins test builds

Retyping parameters bugfix

rebase