Separate the resolving of files into a separate module.
Rewrite the scanning and reading of source files
Start with lib/wrapup that wraps all modules and a simple ascii output
Adding the watch method.
Adding the wrup command, using commander, it supports subcommands
Improve watching files. Cleanup files that are not required anymore.

Now only files that are modified are re-parsed. Those modules are
invalidated and will be parsed again. When require() calls are removed
those modules are removed from the cache too.
Fix output/browser.js
Update Graph output mode
Only require() the required (by --require) initially.
Update amdOneFile (amd-combined) output mode
Cleanup some old unused variables
Update the AMD output mode: wrup amd -r test.js -o dir
Adding the --output option for all output modes
Add all options back, and fix the source field in the loc object of the AST
Change // @sourceMappingURL to // #sourceMappingURL

See https://docs.google.com/document/d/1U1RGAehQwRypUTovF1KRlpiOFze0b-_2gc6fAH0KY0k/edit#heading=h.lmz475t4mvbx
Make wrapup and output emitters
Better logging and error handling
Remove old files
Make lib/main a factory function
Fix typo in namespace