This is wonderful, sadhu, sadhu, sadhu!
Now what I am going to write you certainly know already, but still, it's better to say than not say and miss it... 🙃 I have numbered the points to reduce any potential confusion. 😁
1. Do you know DPR, Digital Pali Reader by ven. Yuttadhammo? https://pali.sirimangalo.org/ In the Dictionary tab, he has there "Atthakatha Dictionary" Is that something that you would like to do? I don't know how he did it, but it is possible to search terms among the Atthakathas inside the Atthakatha texts without any references. It simply "explains" any term that I would type in by the Atthakatha explanation. See screenshots here -
https://ibb.co/ySbksxH
https://ibb.co/vcBJ6Th
https://ibb.co/1M4x5Ln
I found this particularly helpful.
2. Just a little note for you, huge commentarial text for Mula Pali appears also in AN 1 - Etadaggavagga. 😅
3. As for Nidanas, I think they are commentaries for Aṭṭhakavagga in Suttanipata. (But no guarantee. 🙃 ) Oh, that’s Niddesas. I am sorry if I misunderstood. If you mean Mahaniddesa and Culaniddesa, they are basically commentaries for Aṭṭhakavagga. As for nidanas as Pali introductions to Commentareis embedded in almost every Pali Commentary book, I think you do not have to join them with Suttas. They are great alone if you keep the Commentaries available also as standalone texts (like you have done it with Mula Nikayas).
4. I personally use CST4 ( https://www.tipitaka.org/cst4 ), perhaps even more often than an average person would yous his/her phone. I find this software the most useful for scholars like me, who always need to research, debate, and answer controversial Pali issues. CST4 works by paragraphs. For example, you open MN MulapannasaPali, go to paragraph 121 in MN MulapannasaPali, and you have there two buttons in the window - Atthakatha and Tika. If you click to Atthakatha, a new window pops up and shows you the Atthakatha to MN Mulapannasa right in paragraph 121. In Tika, it will pop up a window with Tika right in paragraph 121. (There is no par.121 in the Commentary and Tika, hence it shows the closest par., i.e., 119.) See some screenshots here -
https://ibb.co/gMnQZcz
https://ibb.co/b5wCq95
https://ibb.co/Yb6Z77S
I cannot count the hundreds of hours I saved thanks to this superfast linking. I think you may like to consider this way of referencing, I believe it is simple and very powerful.
5. I think I was not clear with my "suggestion." What I would really wish to find in SuttaCentral (and I am sure thousands of scholars too) is to have the Commentaries (and Sub-Commentaries) database *with translations* . The ever-ready translations are what makes SuttaCentral so valuable for me because when I speak with Czech, Burmese, English, or Pali lay/monks students or scholars, I need to give them translations and the sooner the better. Sometimes I do my own research and cannot be sure about the original Pali, so I look up the translation in Burmese or Sinhalese. But I need to open translations in different PDFs etc., I am sure you know what I mean. 😁 So, the main point in my suggestion was not to include "Commentaries" but rather "Commentaries and their translations."
🌞 I have also seen some posts here in the forum where people ask for translations of Commentaries. I think if SuttaCentral had them in the database it would be just sooooo sweet. 😍
6. I have 5 workers who work fulltime on my large Dhamma projects. (All arranged according to the strictest Vinaya rules.) I cannot promise anything, but I would love to know what are the ways we could help and possibly join your amazing Dhamma endeavors. 🌞