Added to vendor.yml the following dependencies related to automake and autoconf:

- (^|/)configure
- (^|/)configure.ac
- (^|/)config.guess
- (^|/)config.sub

Before changing:
[herbert@vps11071 linguist]$ bundle exec linguist ../atmi++/
75%  Shell
15%  C++
10%  C
0%   Perl

After changing:
54%  C++
37%  C
9%   Shell
0%   Perl

lib/linguist/vendor.yml

@@ -16,6 +16,10 @@
 #  https://github.com/joyent/node
 - ^deps/
 - ^tools/
+- (^|/)configure
+- (^|/)configure.ac
+- (^|/)config.guess
+- (^|/)config.sub
 
 # Node depedencies
 - node_modules/