Merge pull request #124 from ehsteve/code_updates

Simple code updates and gitignore
Make reference list consistent and in one bib file.

Closes sunpy.sunpy-0.4-paper/#121
Add Python package references to introduction.

Closes sunpy/sunpy-0.4-paper#119
Merge pull request #125 from Cadair/references

References
Merge remote-tracking branch 'upstream/master' into code_updates