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2.4 Techniques for Computing Dependencies

There are actually several ways for a build tool like Automake to cause tools to generate dependencies.

This was a commonly-used method in the past. The idea is to run a special program over the source and have it generate dependency information. Traditional implementations of makedepend are not completely precise; ordinarily they were conservative and discovered too many dependencies.
The tool
An obvious way to generate dependencies is to simply write the tool so that it can generate the information needed by the build tool. This is also the most portable method. Many compilers have an option to generate dependencies. Unfortunately, not all tools provide such an option.
The file system
It is possible to write a special file system that tracks opens, reads, writes, etc, and then feed this information back to the build tool. clearmake does this. This is a very powerful technique, as it doesn't require cooperation from the tool. Unfortunately it is also very difficult to implement and also not practical in the general case.
Rather than use the file system, one could write a special library to intercept open and other syscalls. This technique is also quite powerful, but unfortunately it is not portable enough for use in automake.