Before, this would:

1. Not use the correct reference for non-JIRA external trackers.
2. Append 'Closes ' if an external tracker was enabled, but no issue matched the
   branch name.

Use Commit#notes and Note.for_commit_id when possible to make sure we use all the indexes available to us

The `ReferenceExtractor` would return an array of `ExternalIssue`
objects, and then perform `Array#-` to remove the issues
closed. `ExternalIssue`s had `==` defined, but not `hash` or `eql?`,
which are used by `Array#-`.

Also added relevant specs and refactored to_references in a bunch of places to be more consistent.

This method returns the project's ID, making ExternalIssue slightly more
compatible with Issue (which also defines the "project_id" method).

These methods are called quite often in loops so by memoizing their
output we can reduce timings a bit.

The pattern in the `::reference_pattern` class method in the
ExternalIssue model does not match all valid forms of JIRA project
names. I have updated the regex to match JIRA project names with numbers
and underscores. More information on valid JIRA project names can be
found here:
https://confluence.atlassian.com/jira/changing-the-project-key-format-192534.html

* The first character must be a letter,
* All letters used in the project key must be from the Modern Roman Alphabet and upper case, and
* Only letters, numbers or the underscore character can be used.

Now there is a single source of information for which attribute a model
uses to be referenced, and its special character.