What mean file with extension "h.in"?
These files are usually the input for autoconf which will generate final .h files.
Here's an example from PCRE:
#define PCRE_MAJOR @PCRE_MAJOR@
#define PCRE_MINOR @PCRE_MINOR@
#define PCRE_PRERELEASE @PCRE_PRERELEASE@
#define PCRE_DATE @PCRE_DATE@
Autoconf will replace all variables (@…@) with the respective values and the result will be a .h file.
Typically, a .h.in file is a header template that is filled in to become the actual header by a configure script based on the outcome of several tests for features present on the target platform.