Update cells supported for verilog to FIRRTL conversion.

Update cells supported for verilog to FIRRTL conversion.
Issue warning messages for missing parameterized modules and attempts to set initial values.
Replace simple "if (cell-type)" with "else if" chain.
Fix FIRRTL shift handling.
Add support for parameterized modules, $shift, $shiftx.
Handle default output file.
Deal with no top module.
Automatically run pmuxtree pass.
Allow EXTRA_FLAGS and SEED parameters to be set in the environment for tests/tools/autotest.mk.
Support FIRRTL regression testing in tests/tools/autotest.sh
Add xfirrtl files to test directories to exclude files from FIRRTL regression tests that are known to fail.