diff --git a/Build.PL b/Build.PL
index a14b93b..3f63c0c 100644
--- a/Build.PL
+++ b/Build.PL
@@ -45,6 +45,7 @@ my $build = Module::Build->new(
         'perl'        => '5.006',
         'Carp'        => 0,
         'IO::File'    => 0,
+        'Hash::Merge' => 0,
     },
     script_files => [ 'bin/stow', 'bin/chkstow' ],
     all_from => 'lib/Stow.pm.in',
diff --git a/META.json b/META.json
index 2a455a4..dd806c9 100644
--- a/META.json
+++ b/META.json
@@ -17,6 +17,7 @@
       "build" : {
          "requires" : {
             "IO::Scalar" : "0",
+            "Hash::Merge": "0",
             "Test::More" : "0",
             "Test::Output" : "0"
          }
diff --git a/META.yml b/META.yml
index f94d472..9bcbadb 100644
--- a/META.yml
+++ b/META.yml
@@ -4,6 +4,7 @@ author:
   - unknown
 build_requires:
   IO::Scalar: '0'
+  Hash::Merge: '0'
   Test::More: '0'
   Test::Output: '0'
 configure_requires:
diff --git a/bin/stow.in b/bin/stow.in
index fb42dbf..d056cec 100755
--- a/bin/stow.in
+++ b/bin/stow.in
@@ -438,6 +438,8 @@ use Getopt::Long qw(GetOptionsFromArray);
 use Stow;
 use Stow::Util qw(parent error);
 
+use Hash::Merge qw( merge  );
+
 my $ProgramName = $0;
 $ProgramName =~ s{.*/}{};
 
@@ -488,17 +490,29 @@ sub main {
 # Comments  : checks @ARGV for valid package names
 #============================================================================
 sub process_options {
-
-    unshift @ARGV, get_config_file_options();
-    #$,="\n"; print @ARGV,"\n"; # for debugging rc file
-
-    my ($options, 
+    # Get cli options.
+    my ($cli_options, 
         $pkgs_to_unstow, 
         $pkgs_to_stow) = parse_options(@ARGV);
 
+    # Get the .stowrc options.
+    # Note that rc_pkgs_to_unstow and rc_pkgs_to_stow are ignored.
+    my ($rc_options, 
+        $rc_pkgs_to_unstow, 
+        $rc_pkgs_to_stow) = get_config_file_options();
+
+    # Merge .stowrc and command line options.
+    # Preference is given to cli options.
+    # rc options come first in merged arrays.
+    # cli options overwrite conflicting rc options.
+    Hash::Merge::set_behavior('RIGHT_PRECEDENT');
+    my $options = merge($rc_options, $cli_options);
+
+    # Run checks on the merged options.
     sanitize_path_options($options);
     check_packages($pkgs_to_unstow, $pkgs_to_stow);
 
+    # Return merged and processed options.
     return ($options, $pkgs_to_unstow, $pkgs_to_stow);
 }
 
@@ -611,16 +625,14 @@ sub check_packages {
     }
 }
 
-
 #===== SUBROUTINE ============================================================
 # Name      : get_config_file_options()
 # Purpose   : search for default settings in any .stowrc files
 # Parameters: none
-# Returns   : a list of default options
-# Throws    : no exceptions
-# Comments  : prepends the contents of '~/.stowrc' and '.stowrc' to the command
-#           : line so they get parsed just like normal arguments. (This was
-#           : hacked in so that Emil and I could set different preferences).
+# Returns   : (\%rc_options, \@rc_pkgs_to_unstow, \@rc_pkgs_to_stow)
+# Throws    : a fatal error if a bad option is given
+# Comments  : Parses the contents of '~/.stowrc' and '.stowrc' with the same
+#             parser as the command line options.
 #=============================================================================
 sub get_config_file_options {
     my @defaults = ();
@@ -635,7 +647,7 @@ sub get_config_file_options {
             close $FILE or die "Could not close open file: $file\n";
         }
     }
-    return @defaults;
+    return parse_options(@defaults);
 }
 
 #===== SUBROUTINE ===========================================================
@@ -650,7 +662,7 @@ sub usage {
     my ($msg) = @_;
 
     if ($msg) {
-        print "$ProgramName: $msg\n\n";
+        warn "$ProgramName: $msg\n\n";
     }
 
     print <<"EOT";