Ouch.  This is a result of the secondary expansion feature.  The problem is that we defer the tokenization of dependencies until the snap_deps() step, when all the makefiles have been read in.  This means that when we try to override the pattern rule and compare the dependencies, they don't match because our "internal" dependencies are two separate strings "%.w" and "%.ch" (for example) but the overriding dependencies are (at this point) a single string "%.w %.ch".  We don't split them until later.

There are actually a number of problems with the current secondary expansion feature, not least of which is that it wastes memory; I have a half-completed workspace that is changed to always split dependencies right away UNLESS we can show that secondary expansion is a possibility (that is that the .SECONDARYEXPANSION special target is present, AND that the prerequisite list contains expandable elements---contains one or more "$").

Once that change is completed, it will fix this bug as well.

makefile
--start--
all: fred

fred: foo

foo:
        touch fred

#goal to get equivalent of gmake --no-builtin-rules functionality
.SUFFIXES:
#shutoff  implicit rules
(%): %
%.out: %
%:: %,v
%:: RCS/%,v
%:: RCS/%
%:: s.%
%:: SCCS/s.%
%.c: %.w %.ch
%.tex: %.w %.ch
--end makefile--

repro steps:
gmake -p -f makefile.9 > file
in verbose output find section (about line 862)
that starts with # Implicit rules
defect is that the implicit rules for CTANGLE and CWEAVE are not disabled using gmake 3.81

output from gmake 3.81
...
 
# Implicit Rules

(%): %

%.out: %

%:: %,v

%:: RCS/%,v

%:: RCS/%

%:: s.%

%:: SCCS/s.%

%.c: %.w %.ch

%.tex: %.w %.ch

%.c: %.w %.ch
#  commands to execute (built-in):
        $(CTANGLE) $^ $@

%.tex: %.w %.ch
#  commands to execute (built-in):
        $(CWEAVE) $^ $@

# 11 implicit rules, 5 (45.5%) terminal.


--end output --
correct out from gmake 3.80
...
# Implicit Rules

(%): %

%.out: %

%:: %,v

%:: RCS/%,v

%:: RCS/%

%:: s.%

%:: SCCS/s.%

%.c: %.w %.ch

%.tex: %.w %.ch

# 9 implicit rules, 5 (55.6%) terminal.
--end 3.80 output--
gmake -v output
GNU Make 3.81
Copyright (C) 2006  Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.

This program built for x86_64-unknown-linux-gnu

for additional information contact -email is unavailable-