/usr/share/anjuta/templates/java/configure.ac.tpl is in anjuta-common 2:3.18.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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dnl Process this file with autoconf to produce a configure script.
dnl Created by Anjuta application wizard.
AC_INIT([+NameHLower+], [+Version+])
AC_CONFIG_HEADERS([config.h])
AM_INIT_AUTOMAKE([1.11])
AM_SILENT_RULES([yes])
[+IF (=(get "HaveI18n") "1")+]
dnl ***************************************************************************
dnl Internationalization
dnl ***************************************************************************
IT_PROG_INTLTOOL([0.35.0])
GETTEXT_PACKAGE=[+NameHLower+]
AC_SUBST(GETTEXT_PACKAGE)
AC_DEFINE_UNQUOTED(GETTEXT_PACKAGE,"$GETTEXT_PACKAGE", [GETTEXT package name])
AM_GLIB_GNU_GETTEXT
[+ENDIF+]
[+IF (=(get "HavePackage") "1")+]
PKG_CHECK_MODULES(PACKAGE, [[+PackageModule1+] [+PackageModule2+]])
[+ENDIF+]
[+IF (=(get "HaveGtkDoc") "1")+]
GTK_DOC_CHECK([1.0])
[+ENDIF+]
AC_OUTPUT([
Makefile
src/Makefile
[+IF (=(get "HaveI18n") "1")+]po/Makefile.in[+ENDIF+]
])
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