[FEATURE] add chaining consumer

- allows to chain multiple consumers
[DOC] add documentation for chaining
[TEST] add test for MSDataChainingConsumer
[INTERNAL] move code to cpp file
[DOC] better error handling in TOPPDocumenter
improved export of ms2 ground truth

 * all hits are exported in idXML scored/sorted by their intensity contribution
[TEST] extended MSSim test
[FEATURE] add a low memory FileConverter option

- add a low memory option for mzXML/mzML -> mzML conversion
- add an indexed mzML option to produce indexed mzML
[INTERNAL] move last definitions from header file
[TEST,INTERNAL] added test access getMS2Identifications before a simulation was performed

 * fixed segfault if getMS2Identifications but no simulation was performed
[FEATURE] cleanup of transform functions for mzML
[FEATURE] cleanup of transform functions for mzXML
[STYLE] style fix
[DOC] fix docu

fix error in the docu
[FEATURE] added option to PPHiRes to specify which ms levels should be picked
[TEST] added test for selecting spec levels when picking
[PARAM,TOPP] removed ms1_only parameter and replaced with ms_levels
[DOC] documented param change in changelog
[NOP] fixed cppcheck performance warnings
Merge pull request #972 from hroest/fix/FileCleanup

Fix/file cleanup