Removing tagging and all instances of it.

Fixes #2257

This commit introduces helper functions that will be used in a later
commit for caching (running coala only on changed files).

In this commit, coalib.misc.Caching is introduced which contains a
class Cache which contains methods to act as a caching mechanism
that will be useful to determine which files are new or changed and
run coala only on those files to improve coala run time speed.

With `--changed-files` the user can run coala only on those files that
had changed since the last time coala was run. This should improve
the running time of coala.

Fixes #1991