Function and inline statement indentation fixes

I don't like to close multiple bugs in a one shot, but these all tie together and overlap.

Fixes #268
Fixes #275
Fixes #276
Mkdirp when using -o option

Closes #270
Python 1.3.4
1.3.4
Simplify conditional comment formatting

We now treat tags between if-endif conditionals as comments.
This is not ideal, but is significantly better than it was.

Closes #91
Merge pull request #279 from DBCDK/e4x-inline-expression

E4X xml-literal small fixes
Update command-line flags in README
Fix --disable-preserve-newlines not working in python
Merge github.com:einars/js-beautify into e4x-inline-expression