> In addition, we have no universally accepted definition of [**what is part**] of the operating system. 

We could rephrase it thus:

> * "What kinds of modules should be included in an operating system? What kind of modules should be considered **part of an operating system**? 
* "We don't know! There is no universally accepted definition of **what is part** of the typical operating system (and **what is not part** of the typical operating system)." 

Imagine you have a list of 1000 modules: I/O drivers, text editors, graphics procedures etc. And someone asks you: 

> A great collection! But **which are part** of the operating system? 

In your example, the word **what** is used instead of **which** because the number of components that could be included in an operating system is well nigh limitless nowadays, and we are not picking from a list.

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Regarding your idea:

> What I think this is trying to say is probably that there is no agreed-upon definition of what does the term "part of the operation" system mean. If that's the case, then why not say it like this: *In addition, we have no universally accepted definition of what part of the operating system is*.  

Had we wanted to say this, we would've added the indefinite article **a**, because "part" in this sense is a singular count noun:

> We have no universally accepted definition of what is **a** part of the operating system.

Compare: 

> We have no universally accepted definition of what **a** planet is. (or " [...] of what is **a** planet") 

But the word **part** looks a bit awkward here, so we would've more likely used some other phrase:

> We have no universally accepted definition of what is **an** operating system **component**.

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P.S. Kudos to *Stephie* for her comment on the implied clause " [..] and what is *not* part of the OS".

---
P.P.S. Note that there is a slight difference between "part" and "a part". 

> A verb is **a part** of speech. (a discrete piece, a segment, a unit; we stress here this "discretness") 

> Swear words are **part** of my everyday speech. (an intinsic component; the logical stress is on that intrinsic presence of swear words in my speech)  

See some related questions:

* [“As part of” versus “as a part of”](https://english.stackexchange.com/questions/13711/as-part-of-versus-as-a-part-of)  
* [Difference between 'part' and 'a part'?](https://english.stackexchange.com/questions/158232/difference-between-part-and-a-part)  
* ['A part' or 'parts'?](https://ell.stackexchange.com/questions/8350/a-part-or-parts)   
* ['Part of the team' or 'a part of the team'?](https://ell.stackexchange.com/questions/48756/part-of-the-team-vs-a-part-of-the-team)  
* [a part vs. part (duplicate)](https://english.stackexchange.com/questions/117833/a-part-vs-part)  
* [part of life vs. a part of life](https://english.stackexchange.com/questions/127537/zero-article-before-the-word-part-what-is-the-particular-reason-for-this)