Noisy Circuits Improvements

[IsaacP1234]

Improving and documenting pretrajectories and related functionality

If you want to submit an unfinished piece of work in order to get comments and discuss, please mark the pull request as a draft and ping the repository maintainer.

Please address only one topic or issue per pull request! Many small PRs are much easier to review and merge than one large PR.

Before merging, all changes and new functionality should be marked in the CHANGELOG file, but feel free to just leave your CHANGELOG notes in the PR description, to avoid merge conflicts with other requests modifying that file. The maintainer will add these CHANGELOG notes for you if you do so.

Before considering your pull request ready for review and merging make sure that all of the following are completed (please keep the clecklist as part of your PR):

• The code is properly formatted and commented.
• Substantial new functionality is documented within the docs.
• All new functionality is tested.
• All of the automated tests on github pass.
• We recently started enforcing formatting checks. If formatting issues are reported in the new code you have written, please correct them. There will be plenty of old code that is flagged as we are slowly transitioning to enforced formatting. Please do not worry about or address older formatting issues -- keep your PR just focused on your planned contribution.

If possible, keep your git history not too wild (rebase and squash commits, keep commits small and semantically separated) so that review is easier.

[Fe-r-oz]

Hi Isaac,

It seems the merge conflicts might have arisen because commits from your previous PR have resurfaced.

Stefan's note: fix the merge conflicts here without doing cherrypicks or rebases or anything like that. The merge conflicts seem reasonably small, so this solution might be easiest.

With regards to your mermaid schematic link:

https://mermaid.ink/img/pako:eNq1lltvmzAUgP-K5T60k6DiFrogbS_r9raLljxUCXkwxiRWDI58WRc1_e91MVlIyzRteH4JHH_n41g6jv0AMS8JzGDeVIzf4w0SCsxv8waYIRVSZHl3BxaLFfD994cZrTVDivIGRIe1mQzR1fLDl69zEHrx6s2fs2KbVfxdVmiz8OssW4PlNcZEykMbi451RV5yxhYDbPEbFgP_2sAfheCiQ_EwGp2XIIjUTEXL7-3vqscVfaXF4gEMD-jCc64LGk7q-mo503UXkgA1JZD7uuCMYrATvEAFZVQReSy5q8_m9kNxP2QezOsPxDSRy289jZ0-jbnQBHTFAvAOBNfTIJ4k6UvuE6JMCwIsE8TpJEinryEmT7YWnCQ3aZCsjn2yZ8R2C6goY9lF1Q4PVLxRfoVqyvYZuJwRQatLTyrBtyS7CNrRV3StM95ROHDg8Y7IwVoiB2uJRq6la2wXksiFJB4nMbtonMBuwH91MNpsZ60nAOfzHe7f01JtsnD308OccZEVDOGtN_SBl8bQuTFyboydGxPnxolzY-rceOPc-Na5ceq-w__DpnG_a8Lx2wZ6sCaiRrQ0V8GH5w_kUG1ITXKYmceSVMj8FebmlvhoUKQVn-0bDDNljn4PCq7XG5hVz0e3B_WuNMfALUVrgepf0R1qFpyf3klJFRef7eWzvYM-PgGgdnFL?type=png)](https://mermaid-js.github.io/mermaid-live-editor/edit#pako:eNq1lltvmzAUgP-K5T60k6DiFrogbS_r9raLljxUCXkwxiRWDI58WRc1_e91MVlIyzRteH4JHH_n41g6jv0AMS8JzGDeVIzf4w0SCsxv8waYIRVSZHl3BxaLFfD994cZrTVDivIGRIe1mQzR1fLDl69zEHrx6s2fs2KbVfxdVmiz8OssW4PlNcZEykMbi451RV5yxhYDbPEbFgP_2sAfheCiQ_EwGp2XIIjUTEXL7-3vqscVfaXF4gEMD-jCc64LGk7q-mo503UXkgA1JZD7uuCMYrATvEAFZVQReSy5q8_m9kNxP2QezOsPxDSRy289jZ0-jbnQBHTFAvAOBNfTIJ4k6UvuE6JMCwIsE8TpJEinryEmT7YWnCQ3aZCsjn2yZ8R2C6goY9lF1Q4PVLxRfoVqyvYZuJwRQatLTyrBtyS7CNrRV3StM95ROHDg8Y7IwVoiB2uJRq6la2wXksiFJB4nMbtonMBuwH91MNpsZ60nAOfzHe7f01JtsnD308OccZEVDOGtN_SBl8bQuTFyboydGxPnxolzY-rceOPc-Na5ceq-w__DpnG_a8Lx2wZ6sCaiRrQ0V8GH5w_kUG1ITXKYmceSVMj8FebmlvhoUKQVn-0bDDNljn4PCq7XG5hVz0e3B_WuNMfALUVrgepf0R1qFpyf3klJFRef7eWzvYM-PgGgdnFL

For implementation, embed the Mermaid chart within <div class="mermaid"></div> tags. You can also render it directly in the browser using some HTML, allowing you to verify its appearance—particularly if you're using a custom color palette.

Here's an example of the syntax for docstring rendering:

```@raw html
<div class="mermaid">
graph TB

</div>

It’s just my observation, but using the default color palette in Mermaid allows it to render nicely in both dark mode and light mode without any additional adjustments. However, if you choose to apply your own custom color scheme, you’ll need to verify how it appears in both light and dark modes to ensure it looks good across both themes.

Regarding the addition of a Mermaid schematic, you can refer to QuantumSavory for inspiration: https://quantumsavory.github.io/QuantumSavory.jl/stable/register_interface/. On a related note, click the ⚙️ button, select "documenter-dark" if you are not using dark mode and let me know if all the boxes in the QS Mermaid charts are clearly readable. I am unable to read the text in white for Mermaid charts in the aforementioned link in dark mode. I've switched browsers and operating systems, but this issue still occurs when using dark mode or documenter-dark mode. Apologies for the slight digression.

Edit: This is due to the <code></code> style tags being used in register_interface.md. In the how to guide for first gen repeater experiments, <code> tags are not used and the mermaids chart are displayed correctly in the dark mode. Hence, please refer to firstgenrepeater.md instead of register_interface.md for the time being.