Clang format the code base

[juntuu]

There was almost no problems with clang-format (one group of macros got globbered to one), although I disabled include sorting for the run, as it had previously generated some issues.

I ran the tool with

clang-format --style=file --sort-includes=false --verbose  <filenames>

Accidentally excluded few files at first from formatting, added those now (base64 is still deliberately left out)

Also removed jep.c as it was not used anywhere as far as I could see