Documentation updates and bugfixes

[LonnekeScheffer]

Documentation improvements:

• Primarily: better documentation for developer tutorials --- better intro ("why" should you integrate into immuneML) --- rewritten tutorials in more detail --- dummy examples of new components (SillyEncoder, Sillyclassifier, etc), with minimal clutter

• Some re-organisation and revisiting of old docs

• Improved/updated figures (e.g., explanation of YAML structure, valid YAML component combinations)

• Reformatting of class docs (bold), added missing docs

• Changes to e.g., MLMethod and DatasetEncoder interfaces to make integration of new components more streamlined

• removed unfinished WeightsDistribution report that shouldnt have been there

• simplified bits of code here and there (e.g. removing unused parameters, cleaning up utility methods)

[LonnekeScheffer]

To do before reopening:

• resolve KerasSequenceCNN issue on master branch
• make sure tests for 'silly' methods are not executed on github