A collection of minor issue fixes

[djnavarro]

Attempts to fix several small issues. Summary of changes:

• Markdown files renamed to .Rmd and updates .yml file. (issue Rename all files to end in .Rmd #149)
• Fixes tick marks to properly illustrate log scales. (issue p116: log10(mb) gives (probably) not the intended graph #124)
• Adds cross link to clarify reference to ..label.. (issue Various comments/suggestions  #99, item 1)
• Tidies the table illustrating how to add/remove/override aesthetics within layer (issue Various comments/suggestions  #99, item 2)
• Makes the introduction to manual scales section a little cleaner (issue Various comments/suggestions  #99, item 3)
• No changes needed for issue Various comments/suggestions  #99 item 4 as the section is now gone
• Adds a comment early in the text about the relationship between axis limits and summary statistics (fixes Discarding values #23 ... possibly! I wasn't certain where in the text this should be introduced).

[djnavarro]

On reflection, perhaps hold off on reviewing this. I just noticed that #146 is another mechanical fix. I might take care of that one now, and then maybe do something larger (e.g., the rewrites for space-time) in the subsequent PR

[djnavarro]

Okay should be done now (I hope!)

[hadley]

Thanks!!