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Default long scientific document

Hello,

I'm now writing my Master of Science Thesis and till now I used Master and
Subdocuments for it (all chapters in separate subdocuments). Today I've
come accross several articles that I must say frightened me, saying that
there are major problems with Master documents (on word.MVPS.Org site).

So if there are such problems with them what should I do now? How to write
a long scientific document with loads of equations, figures, bibliography
cross-references. If I keep it all in one document and it becomes larger
than 30 pages (with many equations) work with it becomes very unpleasent

What are other methods of handling large scientific documents without the
problem considering corrupted master documents?

--
Wojtek Kurek