Here is a list of all files with brief descriptions:

[detail level 1234]

doc
doxygen
install
common-cmake-parameters.doxygen
install-contrib.doxygen
install-linux.doxygen
install-macs.doxygen
install-testing-openms.doxygen
install-win.doxygen
public
Changelog.doxygen
commit_messages.doxygen
developer_coding_conventions.doxygen
developer_cpp_guide.doxygen
developer_faq.doxygen
developer_how_to_write_tests.doxygen
developer_tutorial.doxygen
ExternalCode.doxygen
Main.doxygen
Modules.doxygen
PyOpenMS.doxygen
TargetedQuantitation.doxygen
TOPP.doxygen
TOPPAS.doxygen
user_FAQ.doxygen
GUITOOLS
FLASHDeconvWizard.cpp
INIFileEditor.cpp
SwathWizard.cpp
TOPPAS.cpp
TOPPView.cpp
MISC
QApplicationTOPP.cpp
FLASHDeconvWizardBase.cpp
INIFileEditorWindow.cpp
SwathWizardBase.cpp
TOPPASBase.cpp
TOPPViewBase.cpp
AccurateMassSearch.cpp
AssayGeneratorMetabo.cpp
AssayGeneratorMetaboSirius.cpp
BaselineFilter.cpp
ClusterMassTraces.cpp
ClusterMassTracesByPrecursor.cpp
CometAdapter.cpp
ConsensusID.cpp
ConsensusMapNormalizer.cpp
CVInspector.cpp
DatabaseFilter.cpp
DatabaseSuitability.cpp
Decharger.cpp
DecoyDatabase.cpp
DeMeanderize.cpp
Digestor.cpp
DigestorMotif.cpp
DTAExtractor.cpp
EICExtractor.cpp
Epifany.cpp
ExecutePipeline.cpp
ExternalCalibration.cpp
FalseDiscoveryRate.cpp
FeatureFinderCentroided.cpp
FeatureFinderIdentification.cpp
FeatureFinderLFQ.cpp
FeatureFinderMetabo.cpp
FeatureFinderMetaboIdent.cpp
FeatureFinderMultiplex.cpp
FeatureLinkerBase.cpp
FeatureLinkerLabeled.cpp
FeatureLinkerUnlabeled.cpp
FeatureLinkerUnlabeledKD.cpp
FeatureLinkerUnlabeledQT.cpp
FileConverter.cpp
FileFilter.cpp
FileInfo.cpp
FileMerger.cpp
FLASHDeconv.cpp
FuzzyDiff.cpp
GenericWrapper.cpp
GNPSExport.cpp
HighResPrecursorMassCorrector.cpp
IDConflictResolver.cpp
IDDecoyProbability.cpp
IDExtractor.cpp
IDFileConverter.cpp
IDFilter.cpp
IDMapper.cpp
IDMerger.cpp
IDPosteriorErrorProbability.cpp
IDRipper.cpp
IDRTCalibration.cpp
IDScoreSwitcher.cpp
IDSplitter.cpp
ImageCreator.cpp
INIUpdater.cpp
InternalCalibration.cpp
IonMobilityBinning.cpp
IsobaricAnalyzer.cpp
IsobaricWorkflow.cpp
JSONExporter.cpp
LuciphorAdapter.cpp
MapAlignerIdentification.cpp
MapAlignerPoseClustering.cpp
MapAlignerTreeGuided.cpp
MapNormalizer.cpp
MapRTTransformer.cpp
MapStatistics.cpp
MaRaClusterAdapter.cpp
MascotAdapterOnline.cpp
MassCalculator.cpp
MassTraceExtractor.cpp
MetaboliteAdductDecharger.cpp
MetaboliteSpectralMatcher.cpp
MetaProSIP.cpp
MRMMapper.cpp
MRMPairFinder.cpp
MRMTransitionGroupPicker.cpp
MSFraggerAdapter.cpp
MSGFPlusAdapter.cpp
MSstatsConverter.cpp
MultiplexResolver.cpp
MzMLSplitter.cpp
MzTabExporter.cpp
NoiseFilterGaussian.cpp
NoiseFilterSGolay.cpp
NovorAdapter.cpp
NucleicAcidSearchEngine.cpp
OpenMSDatabasesInfo.cpp
OpenMSInfo.cpp
OpenNuXL.cpp
OpenPepXL.cpp
OpenSwathAnalyzer.cpp
OpenSwathAssayGenerator.cpp
OpenSwathChromatogramExtractor.cpp
OpenSwathConfidenceScoring.cpp
OpenSwathDecoyGenerator.cpp
OpenSwathDIAPreScoring.cpp
OpenSwathFeatureXMLToTSV.cpp
OpenSwathFileSplitter.cpp
OpenSwathMzMLFileCacher.cpp
OpenSwathRewriteToFeatureXML.cpp
OpenSwathRTNormalizer.cpp
OpenSwathWorkflow.cpp
PeakPickerHiRes.cpp
PeakPickerIM.cpp
PeakPickerIterative.cpp
PeptideDataBaseSearchFI.cpp
PeptideIndexer.cpp
PercolatorAdapter.cpp
PhosphoScoring.cpp
ProteinInference.cpp
ProteinQuantifier.cpp
ProteomicsLFQ.cpp
PSMFeatureExtractor.cpp
QCCalculator.cpp
QCEmbedder.cpp
QCExporter.cpp
QCExtractor.cpp
QCImporter.cpp
QCMerger.cpp
QCShrinker.cpp
QualityControl.cpp
QuantmsIOConverter.cpp
Resampler.cpp
RNADigestor.cpp
RNAMassCalculator.cpp
RNPxlXICFilter.cpp
SageAdapter.cpp
SeedListGenerator.cpp
SemanticValidator.cpp
SequenceCoverageCalculator.cpp
SimpleSearchEngine.cpp
SiriusExport.cpp
SpectraFilterNLargest.cpp
SpectraFilterNormalizer.cpp
SpectraFilterThresholdMower.cpp
SpectraFilterWindowMower.cpp
SpectraMerger.cpp
SpectraSTSearchAdapter.cpp
StaticModification.cpp
TargetedFileConverter.cpp
TextExporter.cpp
TICCalculator.cpp
TriqlerConverter.cpp
XFDR.cpp
XMLValidator.cpp