[FIX] IDPep: remove unused output files, better naming; gnuplot script now writes PDF instead of PS (better platform support); fixed some bugs which lead to SegFault when q-values are provided (from FDR upstream)
fixed gcc compile errors
fixed 'out_plot' from required to optional'
[BUILD] added clang warnings as suggested in #652
[INTERNAL,BUILD] restructured include_directories calls

 * we now distinguish between internal and SYSTEM includes and instruct the compiler to ignore system includes
 * note that everything that doesn't come from the current package will be treated as system (e.g., OpenSwathAlgo is SYSTEM from OpenMS' point of view)
 * renamed include directories variables to match the name of the corresponding target (preparation for export stuff)

I additionally removed an unused CMakeLists.txt file from openswathalgo
[FIX] suppress plots when not requested
added a comment
[NOP] fixed a couple of unreachable-code warnings
[BUILD] reduced number of warnings by disabling doc related warnings

 * -Wdocumentation-unknown-command
 * -Wdocumentation
[NOP] checker fix
[FIX] expose additional parameter on the CLI
added missing include
[FIX,NOP] fixed all the -Wextra-semi warnings reported by clang
[FIX] amend previous commit
Merge pull request #726 from cbielow/IDPEP++

IDPosteriorErrorProbability fixes
Merge pull request #735 from aiche/feature/clang-warning-level

[FEATURE] clang warning level