[top_darjeeling] Don't generate clk_io_root and clk_io_div2_root in clkmgr

### desc

These two clocks are unused and should not be generated in the first place. Right now, we need to waive lint warnings associated with that (see #25982). Since ipgen is already used to generate clkmgr, it should be doable but there is some work in the templates / hjson files.

Start by tracing how ipgen generates clkmgr from its templates and HJSON files, focusing on clk_io_root and clk_io_div2_root. Confirm where these clocks are described and how the generated output is checked. Done means the unused clocks are no longer generated and the related lint waivers are no longer needed.

Written by the indexing model from the issue text.