Look for plugins under the source directory

When generating the site, Jekyll will now look for plugins under the
source directory by default. The plugin location can still be changed in
_config.yml
Merge remote-tracking branch 'upstream/master' into issue-653
Look for plugins under the source directory by default
Add TomDoc
Merge branch 'master' into issue-653
Merge branch 'master' into issue-653
Add back a test that was mistakenly removed.
Rename setup_plugins to plugins_path
Fix up the whitespace.

Remove an extra blank line and fix another whitespace error pointed out
by git diff
Merge pull request #654 from mattr-/issue-653

Look for plugins under the source directory. Fixes #653.