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I had an issue that can be replayed with the current example snippets: You have the snippets 'alias:add' and 'sshconfig:add' in shell.yml, 'user:add' in mysql.yml and 'vhost:add' in apache.yml.
If you run 's run add' it promptly runs 'user:add' as it is the nearest match. I think the ':'-separator should be respected and it should recognize all 4 snippets as equal concerning the query for just 'add' and report 'Multiple Snippets matched'.
Great project, btw. It really helps in my day-to-day work. :)