Use final sanitized (and disambiguated in the future) alias name instead of the user-specified alias

Co-authored-by: mergify[bot] <37929162+mergify[bot]@users.noreply.github.com>

* Allow IntrinsicModule to be used in Instantiate

Change a few `RawModule`s to `BaseModule`s to allow for intrinsic
modules to be used with the instantiation API.

* Add tests for Instantiate of non-RawModules

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Co-authored-by: Fabian Schuiki <fabian@schuiki.ch>

This enables Chisel users to use these newer Scala versions.

Fix up code underlying `compile` used in many tests to
put annotations at the head of chirrtl
removed writing of WriteOutputAnnotations
removed passing in of json created by WriteOutputAnnotations files to firtool
Moved two tests in TraceSpec to use in instead of ignore

Fix a bug in BoringUtils (and secret IO APIs) where APIs would return a
Data.  This could create problems if the BoringUtils APIs were used
directly in operations, e.g., the following could cause a problem:

    val a = b & BoringUtils.bore(c)

This requires some casting of DontCare as it is unfortunately not a proper
"bottom" type.

No test is added as the test is that Scala passes type checking.

Signed-off-by: Schuyler Eldridge <schuyler.eldridge@sifive.com>

The updated versions fix warnings about deprecated actions.

Change FIRRTL emission to use a simpler syntax for registers without a
reset.  Previously, this used a self-reset with a zero reset signal.
Simplify this to emit a register without a reset.

Signed-off-by: Schuyler Eldridge <schuyler.eldridge@sifive.com>

Co-authored-by: Jack Koenig <koenig@sifive.com>

* Add Top-level parameterized reset type
* Add the ability to set the top reset type for any Module

Make the lines of code that need to be touched in the template fewer