Fix temp_dir parse error and add features for Yosys+Parmys

Description

This PR fixed the issue for #2347, which may cause Parmys+Yosys synthesize failure.
This PR also adds two features for #2351
Since the VTR project moves to Parmys+Yosys front end, more people are likely to write projects using SystemVerilog and use the include syntax to organize projects, so I added the command line support for letting Yosys search for the include directory.
In addition, I added support for manually specifying the top module for Yosys, in case sometimes Yosys find the wrong top module hierarchy.

Related Issue

#2347
#2351

Motivation and Context

I am doing my project with VTR and using SystemVerilog as my main language, so I added the two features to support wider use.

How Has This Been Tested?

Tested on Ubuntu 22.04 LTS.

Types of changes

• Bug fix (change which fixes an issue)
• New feature (change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My change requires a change to the documentation
• I have updated the documentation accordingly
• I have added tests to cover my changes
• All new and existing tests passed
  The -top seems to exist in the document https://docs.verilogtorouting.org/en/latest/parmys/parmys_plugin/, but was not supported in the command line, so I added this.
  The include dir needs a documentation change to let people know this feature.