Many folks prefer writing different sections of the paper in separate tex files and including them in the main document using the include directive. This has several advantages:

1. Coauthors often feel comfortable working on their individual sections.
2. Makes versioning a little easier.
3. Navigating is less painful.

There are situations where merging those sections into a single document is needed. For example, when some publications ask you to limit the number of files. After a little bit googling, this good old perl script seems to get the job done. To merge multiple sections run

    perl latexpand main.tex > merged.tex