Linearize top-level-directory dependencies

[Strilanc]

There were some cyclic dependencies between top level directories. This change refactors the locations of some files and methods to restore a linearized dependency ordering.

It also does some renaming, like stim_benchmark -> stim_perf.

Note that .test.*, .perf.*, and .pybind.* files are outside the order.

A current linearized order is:

• stim/mem
• stim/util_bot
• stim/gates
• stim/stabilizers
• stim/circuit
• stim/dem
• stim/io
• stim/gen
• stim/simulators
• stim/util_top
• stim/diagram
• stim/cmd