Refactor JCDB, File and fix bug related to logic preprocessing

Closes #1003

See merge request frama-c/frama-c!3023

Aorai for Eva Analyses

See merge request frama-c/frama-c!2952

Feature/andre/fc script list functions

See merge request frama-c/frama-c!2442

and -aorai-no-generate-annotations

also avoid accidental `*/` in FILTER command

and start debugging the issues found...

- No more generation of C file without `-print`
- Remove mention of deleted option `-aorai-output-c-file`
- No reference to Jessie anymore. Use WP instead

If you want to see instrumented code use `-then-last -print [-ocode file.c]`
like everyone else.

Also properly indent some files