Always process metadata using the merge file.

Instead of reading the merge OR the shells first, always read from the merge file and read the shells file to get indent information.
Do a better job with indent and .5/.7 columns.

Also alpha-sort by table ID to make future diffs easier.
Store the whole table/column data so it can be sorted.
Fix broken 2009 header column data.
Fix 2009 3yr header problems.
Merge pull request #3 from censusreporter/always-process-merge

Always process using merge file