Well, this is more than and ordinary shell script - its a makefile. While I wouldn't want to rewrite a makefile in perl, you could simplify the genfiles recipe by replacing the shell script there with a perl script.

The recipe for genfiles basically does this

chdir to src
foreach basename of "*.pdl" files
    if( $basname.cxx does not exist )  or 
      ( $basname.pdl is newer than $basename.cxx )
    then
        execute NOIPGEN on $basename.pdl outputting 
        stderr and stdout to $OBJDIR/noipgen.err
    endif
endfor

if( $OBJDIR/noipgen.err exists )
then
    mv the noipgen.err file to noipgen.debug
endif

chdir to src
foreach basename of "*mdl" files
    if( $basname.cxx does not exist ) or 
      ( $basnemae.mdl is newer than $basname.cxx)
    then
      execute NOIMGEN on $basename.mdl outputting 
      stderr and stdout to $OBJEDIR/noimgen.err
    endif
endfor

if( $OBJDIR/noimgen.err exists )
then
    mv the noimgen.err file to noimgen.debug
endif
[download]

You could easily combine those two things into a perl script and then change the recipe to be something like this:

genfiles: setup
        @my_script pdl $NOIPGEN $OBJDIR noipgen.err
        @my_script mdl $NOIMGEN $OBJDIR noimgen.err
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-derby

update but now that I think about it some more that whole script could be replaced by more generic makefiles recipes that show target files have a dependancies on pdl and mdl files. Check out the make book.