Clang-format; slight code improvements

Code improvements:
 * if(x > n) n = x; => n = max(n, x);
 * Introduce a function for formatted printing
Move the options to a more suitable struct
Make options output more consistent
Clang-format
Evaluation as a class; print best motif occurrence
Rename switch and fix CLI information
Print header line for best motif file
Merge branch 'master' into best_occurrence
Use CMake WARNINGs only when not building the manual
Bump patch number
Split documentation up into multiple files
Fix some typos
Mention tikzlogo
Correct ASCII-casing for LaTeX
Add CLI switch to find best motif occurrences
Header and source for new code
Define new friend relationship
Merge branch 'motif_conditional' into best_occurrence

Conflicts:
	src/hmm/hmm.hpp
	src/hmm/main.cpp
Rename print_best option
Stub code to use conditional motif decoding