By default Debian dh passes --disable-dependacy-tracking when building.
If the package rules also adds --builddirectory to use out of source builds
(eg. "dh $@ --builddirectory=build --parallel --with autoreconf"), and the
package happens to be using subdir-objects automake option and generated source
files from lex/yacc then the build will fail.

Eg.

mkdir build
../configure --disable-dependency-tracking --disable-silent-rules
make

/bin/bash ../ylwrap ../src/scanner.ll lex.yy.c src/scanner.cc -- flex
../ylwrap: line 206: ../src/scanner.cc: No such file or directory
Makefile:422: recipe for target 'src/scanner.cc' failed
make: *** [src/scanner.cc] Error 1

A simple patch to lex.am and yacc.am fixes this.

This broken in both Jessie and Stretch/Sid. It would be good to see it fixed in
all.

On Fri, 4 Dec 2015 13:50:22 +0000 Nicholas Brown  <nickbroon+debbug@gmail.com> wrote:
 > Package: automake
 > Version: 1:1.14.1-4
 > Severity: important
 > Tags: upstream patch
 >
 > By default Debian dh passes --disable-dependacy-tracking when building.
 > If the package rules also adds --builddirectory to use out of source
builds
 > (eg. "dh $@ --builddirectory=build --parallel --with autoreconf"),
and the
 > package happens to be using subdir-objects automake option and
generated source
 > files from lex/yacc then the build will fail.
 >
 > Eg.
 >
 > mkdir build
 > ../configure --disable-dependency-tracking --disable-silent-rules
 > make
 >
 > /bin/bash ../ylwrap ../src/scanner.ll lex.yy.c src/scanner.cc -- flex
 > ../ylwrap: line 206: ../src/scanner.cc: No such file or directory
 > Makefile:422: recipe for target 'src/scanner.cc' failed
 > make: *** [src/scanner.cc] Error 1
 >
 > A simple patch to lex.am and yacc.am fixes this.
 >
 > This broken in both Jessie and Stretch/Sid. It would be good to see
it fixed in
 > all.
 >
 >
 >

Upstream automake development is currently dormant. How to proceed?

I've submitted this up stream as:
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=27188