[topgen] ipgen template files (*.hjson.tpl) are used for clock and reset checks

[Razer6]

The current topgen implementation uses the ipgen template files, the unrendered *.hjson.tpl files, for the initial clock and reset connection checks.

This approach is problematic because an ipgen'ed IP might want to enable or disable certain clk/reset signals in their configuration. Let's say you have an IP that has two different configurations:

1. Config # 1 2 clocks
2. Config # 2 1 clock

Let's say a top uses config # 2 with one clock. The top-level HJSON will then only specify 1 clock in their connection. However, during the initial clock checks, topgen will use the *.hjson.tpl file for the checks. There, 2 clocks for both configs are specified. The check then fails because the top has only connected 1 clock. Obviously, that is correct.

The code in question for that issue is in here:

https://github.com/lowRISC/opentitan/blob/4e65b642c74d3f89ead7e6717fc4231c5397bf77/util/topgen.py/L703-L745

@matutem I'ma assigning to you, since we chatted about that in Slack