debian/patches/fix_main_makefile.patch

@@ -259,7 +259,7 @@
  
  build: arb
 -	$(MAKE) binlink preplib compile_compatibility
-+	$(MAKE) core
++	$(MAKE) db core
  
  all:
  	@echo "Build time" > $(TIMELOG)

debian/patches/ignore_unneeded_stuff.patch

 --- a/SOURCE_TOOLS/generate_all_links.sh
 +++ b/SOURCE_TOOLS/generate_all_links.sh
+@@ -1,7 +1,7 @@
+ #!/bin/bash
+ 
+ SELF=$ARBHOME/SOURCE_TOOLS/generate_all_links.sh
+-READLINK=${ARBHOME}/SH/arb_readlink
++READLINK=readlink
+ 
+ 
+ finderr() {
 @@ -126,7 +126,9 @@ makedir lib/help &&
  (test -z $MOTIF_LIBPATH || symlink_file $MOTIF_LIBPATH lib/libXm.so.3) &&
  
@@ -164,7 +173,7 @@
  defined $revision || die "expected known revision!";
 --- a/Makefile
 +++ b/Makefile
-@@ -1625,7 +1625,7 @@ redo_links: clean_links
+@@ -1624,7 +1624,7 @@ redo_links: clean_links
  #********************************************************************************
  
  header_libs:
@@ -173,7 +182,7 @@
  
  #********************************************************************************
  
-@@ -1657,7 +1657,7 @@ endif
+@@ -1656,7 +1656,7 @@ endif
  
  
  binlink:
@@ -182,7 +191,7 @@
  
  preplib:
  	(cd lib;$(MAKE) all)
-@@ -1924,7 +1924,7 @@ arb_external: convert tools gde readseq
+@@ -1910,7 +1910,7 @@ arb_external: convert tools gde readseq
  arb_no_perl: arbapplications arb_external
  
  arb: 

debian/rules

@@ -37,7 +37,7 @@ config.makefile: config.makefile.template
 
 override_dh_auto_build:
 	ln -s TEMPLATES INCLUDE
-	for header in UNIT_TESTER/*.h ; do ln -s ../$${header} INCLUDE/`basename $${header}` ; done
+	for header in CORE/*.h UNIT_TESTER/*.h ; do ln -s ../$${header} INCLUDE/`basename $${header}` ; done
 	ln -s /usr/include/valgrind/valgrind.h INCLUDE/valgrind.h
 	ln -s ../AISC_COM/AISC PROBE_COM/AISC
 	mkdir bin