Add rst files as dependency of output directory

Without this, changes to rst (from changes to Org files) were not
changing output with `make site` run.
Use pelican -d flag instead of `make clear`
Remove site dependency for publish target

This resulted in an additional pelican run.
Add site as dependency for view target
Reorder makefile targets
Update makefile phony targets
Update makefile help message

Aside from adding less line, all changes are just formatting, order, and
wording.
Correct typo in post