This updates PyflakesTool to subclass the newer BaseTool, and to use

the newer features it offers (dependencies, centralized base command

building, and standardized error code/column output).
It also fixes some mistakes from my prior pyflakes change. It turns out

pyflakes has some inconsistencies with a colon found in the generated

output, and this led to issues with parsing some of the output.
On top of this, execute()'s return_errors combined with

split_lines didn't do the right thing when using with_errors=True

(the default). That's been corrected to give return_errors precedence.
These were caught by the new integration tests, which are also added in

this change.

All unit tests pass on Python 2.x and 3.x.