engine2 -> engine
s/engine2/engine/g

... to match the renamed module.
tools/performance/serialization_speedtests:

Removed.
tests/db/model_risk_exposure_test:

Use hazardlib.geo instead of shapes.
tests/shapes_test:

Removed the test module for `shapes`.
.classpath:

Why is this still here?
docs/source/shapes.rst:

Deleted.
docs/source/index.rst:

Removed `shapes` from ToC.
tools/cluster:

Removed obsolete cluster scripts.
bin/oq_restart_workers:

Removed obsolete script.
job:

Deleted config and params modules.
tests/db/model_risk_exposure_test:

Fixed some semantic errors with site geometry.
tests/utils/helpers:

Removed the unused `store_hazard_logic_trees`.
calcs/hazard/general:

Removed `store_source_model` and `store_gmpe_map`.
shapes: Removed.
writer:

Removed a handful of unused classes.