Removed usage of directory local variables.

Fixes #12 and #42.
Added better paragraph filling.

Text fills better around Doxygen @param et al. and text in comments now
do auto-fill.

Fixes #5.
Prepared for .api.php CoderSniffer sniffs.
Made it possible to refer to issue comments.

The convention to put issue numbers in brackets at patches and have the
issue number be a clickable link, i.e:

  projects[ctools][patch][1277908] = http://drupal.org/files/ctools-uuids_for_exported_objects-1277908-118.patch

is extended so we can have add i.e comment numbers and still have them
clickable, i.e.:

projects[services][patch]['1912842-9'] = http://drupal.org/files/services-rest_server_parse_xml_with_arrays-1912842-9.patch
projects[services][patch]['1912842-13'] = http://drupal.org/files/issues/services-rest_server_parse_xml_with_arrays-1912842
Fixed flymake when real file is in a symlinked dir.

Fixes #14.