Canonicalise input files

[ZedThree]

Sorry, this is a horrible PR. In order to apply other input file fixes more cleanly in #2210, first "canonicalise" the input files:

• nested sections are moved to be under their parent section, while
  preserving relative order
• empty sections are removed
• floating point numbers may have their format changed, although the
  value will not change
• consecutive blank lines will be reduced to a single blank line
• whitespace around equals signs will be changed to exactly one space
• trailing whitespace will be removed
• comments will always use '#'

Essentially just a round-trip of input file -> python BoutOptions -> input file, with no other changes.

Viewing this PR with "hide whitespace" enabled will be useful.

The majority of the changes are like:

- zeta = 2.15e-3
+ zeta = 0.00215
- dx = 1.
+ dx = 1.0

This PR does mean any future input file changes will have much cleaner diffs!

[johnomotani]

Mostly looks good. A few small niggles to do with deleting (or not) commented-out options.

[ZedThree]

Meant to try out the new [skip ci] in that commit, oh well

[johnomotani]

Found a few extra orphaned lines to remove.

[ZedThree]

Lovely, thanks @johnomotani !