Wouldn't it make sense to set site.source to the absolute path of the dir where the jekyll command is run (if no config['site'] is specified).
I had some templates where it complained about non existing ./_includes - not sure when exactly though - until I specified the source dir in my config.
Hmm, this probably makes sense. If you could whip up a patch or a good way to test this I'd be up for it.
This is easy to fix. I had problems using includes from within includes (in the _includes directory).
I fixed this issue by changing line 38 in http://github.com/mojombo/jekyll/blob/master/lib/jekyll.rb from:
'source' => '.',
'source' => Dir.pwd,
This change breaks ./test/test_configuration.rb. To fix the test change line 6 in test_configuration.rb to:
@path = File.join(Dir.pwd, '_config.yml')
I can create a patch if required.
If you're still up for making a patch and test for this, that would be awesome.
This is fixed in master.