Editing a file outside atom instance causes issues when reopening

[AgentAntelope]

Steps to reproduce:

1. open atom with atom .
2. open styles.less
3. quit atom
4. move directory
5. open atom with atom .
6. delete parts of styles.less
7. quit atom again
8. return to the first directory
9. reopen atom with atom ., causing styles.less to be opened automatically
10. Colours are highlighted in the wrong places.

[abe33]

Thanks for the report. I'm not sure if it's a problem with the highlights or with the underlying markers, I'll have to dig a bit into it.