Avoid deleting bp2build directory

With this CL, we avoid deleting the bp2build directory and regenerating
all BUILD files. Instead, we regenerate BUILD files which have changes
on the filesystem, and delete old BUILD files which should no longer
exist.

This improves incremental Bazel server performance by about ~5 seconds.
Previously, Bazel would have cache misses for regenerated packages, and
would thus need to analyze them even if no meaningful changes took
place.

For ease of implementation, we avoid removing stale (empty) directories
from the bp2build workspace, but this should have no effect on the
build. (These will be removed on next clean)

Test: New integration tests
Test: Manual benchmarking in conjunction with persistent bazel server
Change-Id: I3e489ff403be34040122876012329060a2506366