Update config migration script with new scalac plugin options.

Reviewed at https://rbcommons.com/s/twitter/r/1218/
Ensure proper semantics when replacing all tasks in a goal.

Testing Done:
ci in flight.

Reviewed at https://rbcommons.com/s/twitter/r/1220/
Take proper care with the order of operations when replacing tasks.

This logic is fragile and should probably be removed entirely.

Testing Done:
Manually verified that this fixes foursquare.web's issues with replacing all tasks in a goal.

ci running.

Reviewed at https://rbcommons.com/s/twitter/r/1221/
Revert conversion of thrift_linter.py to new options format, left in place TODO about precedence of override in target

Testing Done:
PANTS_DEV=1 ./pants goal test tests/python/pants_test/tasks:thrift_linter_integration   passes again

Bugs closed: 727

Reviewed at https://rbcommons.com/s/twitter/r/1223/
Read arguments for thrift-linter from pants.ini.

This allows changing linter options without changing pants.

Testing Done:
./build-support/bin/ci.sh

PANTS_DEV=1 ./pants goal thrift-linter testprojects/src/thrift/com/pants/testproject:thrift-java

Bugs closed: 719

Reviewed at https://rbcommons.com/s/twitter/r/1215/
Add support for updating the environment from prep_commands.

Reviewed at https://rbcommons.com/s/twitter/r/1222/