the reason some of the local modifications went away is just because your generated files are identical to the generated files the author of the ./srclib/ libraries generated with his/her local toolchain (most likely because you are using close to the same version of toolchain).
for a list of file dependencies... you can view... http://matt-massie.com/docs/autobook-1.3/autobook_276.html#SEC276i actually copied and pasted all the ascii art into a single page to print and tape on the wall next to my desk to help keep things straight in my mind. it's not very intuitive.
user input files optional input process output files
================ ============== ======= ============
acinclude.m4 - - - - -.
V
.-------,
configure.in ------------------------>|aclocal|
{user macro files} ->| |------> aclocal.m4
`-------'
aclocal.m4 - - - - - - - .
(acconfig.h) - - - -. |
V V
.----------,
configure.in ----------------------->|autoheader|----> config.h.in
`----------'
.--------,
| | - - -> COPYING
| | - - -> INSTALL
| |------> install-sh
| |------> missing
|automake|------> mkinstalldirs
configure.in ----------------------->| |
Makefile.am ----------------------->| |------> Makefile.in
| |------> stamp-h.in
.---+ | - - -> config.guess
| | | - - -> config.sub
| `------+-'
| | - - - -> config.guess
|libtoolize| - - - -> config.sub
| |--------> ltmain.sh
| |--------> ltconfig
`----------'
aclocal.m4 - - - - - -.
V
.--------,
configure.in ----------------------->|autoconf|------> configure
`--------'
-matt
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