Use latexmk clean functions in Makefile

Remove second check for *.tex files in the dirs
the wildcard should already ensure their existence
Remove unused alpha channels from some png screenshots

This also fixes a `libpng: iCCP: known incorrect sRGB profile` error
Highlight/fade parts of images for data retrieval
Add text about looking into data and getting traces

Fix some references
Fix size of images (was to big)
Add link to documentation
Replace \nikhef by Nikhef
Fix bad color profile in png images (caused by Preview or Alpha
channels..)