bugfix: cc should not add -L or -Wl,-rpath in compile-only mode

- Adding -L and -Wl,-rpath to compile-only command lines ("cc mode" or
  "-c") causes clang (if not also other compilers) to emit warnings that
  confuse configure systems.

- Clang will print warnings about unused command-line arguments.

- This fix ensures that -L and -Wl,-rpath are not added if the compile
  line is just building an object file with -c

- This also cleans up the cc script in several places.

lib/spack/env/cc

@@ -137,10 +137,12 @@ esac
 # libraries.
 if [[ -z $mode ]] || [[ $mode == ld ]]; then
     for arg in "$@"; do
-        if [[ $arg == -v || $arg == -V || $arg == --version || $arg == -dumpversion ]]; then
+        case $arg in
+            -v|-V|--version|-dumpversion)
                 mode=vcheck
                 break
-        fi
+                ;;
+        esac
     done
 fi
 
@@ -164,7 +166,7 @@ fi
 # Set up rpath variable according to language.
 eval rpath=\$SPACK_${comp}_RPATH_ARG
 
-# Dump the version and exit if we're in testing mode.
+# Dump the mode and exit if the command is dump-mode.
 if [[ $SPACK_TEST_COMMAND == dump-mode ]]; then
     echo "$mode"
     exit
@@ -218,9 +220,12 @@ fi
 # It doesn't work with -rpath.
 # This variable controls whether they are added.
 add_rpaths=true
-if [[ ($mode == ld || $mode == ccld) && "$SPACK_SHORT_SPEC" =~ "darwin" ]]; then
+if [[ ($mode == ld || $mode == ccld) && "$SPACK_SHORT_SPEC" =~ "darwin" ]];
+then
     for arg in "$@"; do
-        if [[ ($arg == -r && $mode == ld) || ($arg == -r && $mode == ccld) || ($arg == -Wl,-r && $mode == ccld) ]]; then
+        if [[ ($arg == -r && $mode == ld) ||
+              ($arg == -r && $mode == ccld) ||
+              ($arg == -Wl,-r && $mode == ccld) ]]; then
             add_rpaths=false
             break
         fi
@@ -232,16 +237,21 @@ input_command="$@"
 args=()
 
 #
-# Parse the command line args, trying hard to keep
+# Parse the command line arguments.
-# non-rpath linker arguments in the proper order w.r.t. other command
-# line arguments.  This is important for things like groups.
 #
-# -l arguments are treated as 'other_args' to ensure that they stay in
+# We extract -L, -I, and -Wl,-rpath arguments from the command line and
-# any groups they are a part of. Dependency library -l statements are
+# recombine them with Spack arguments later.  We parse these out so that
-# categorized as 'libs'
+# we can make sure that system paths come last, that package arguments
+# come first, and that Spack arguments are injected properly.
 #
-# The various categories will be recombined with compiler flags into 
+# All other arguments, including -l arguments, are treated as
-# args variable later.
+# 'other_args' and left in their original order.  This ensures that
+# --start-group, --end-group, and other order-sensitive flags continue to
+# work as the caller expects.
+#
+# The libs variable is initialized here for completeness, and it is also
+# used later to inject flags supplied via `ldlibs` on the command
+# line. These come into the wrappers via SPACK_LDLIBS.
 #
 includes=()
 libdirs=()
@@ -316,7 +326,10 @@ while [ -n "$1" ]; do
     shift
 done
 
-# Prepend cppflags, cflags, cxxflags, fcflags, fflags, and ldflags
+#
+# Prepend flags from Spack's cppflags, cflags, cxxflags, fcflags, fflags,
+# and ldflags.
+#
 
 # Add ldflags
 case "$mode" in
@@ -324,15 +337,16 @@ case "$mode" in
         args=(${SPACK_LDFLAGS[@]} "${args[@]}") ;;
 esac
 
-# Add compiler flags.
+# Add C, C++, and Fortran flags
 case "$mode" in
     cc|ccld)
-    # Add c, cxx, fc, and f flags
         case $lang_flags in
             C)
                 args=(${SPACK_CFLAGS[@]} "${args[@]}") ;;
             CXX)
                 args=(${SPACK_CXXFLAGS[@]} "${args[@]}") ;;
+            F)
+                args=(${SPACK_FFLAGS[@]} "${args[@]}") ;;
         esac
         ;;
 esac
@@ -343,30 +357,29 @@ case "$mode" in
         args=(${SPACK_CPPFLAGS[@]} "${args[@]}") ;;
 esac
 
-case "$mode" in cc|ccld)
+# Include all -L's and prefix/whatever dirs in rpath
-        # Add fortran flags
+case "$mode" in
-        case $lang_flags in
+    ld|ccld)
-            F)
+        $add_rpaths && rpaths+=("$SPACK_PREFIX/lib")
-                args=(${SPACK_FFLAGS[@]} "${args[@]}") ;;
+        $add_rpaths && rpaths+=("$SPACK_PREFIX/lib64")
-        esac
         ;;
 esac
 
-# Include all -L's and prefix/whatever dirs in rpath
-$add_rpaths && rpaths+=("$SPACK_PREFIX/lib")
-$add_rpaths && rpaths+=("$SPACK_PREFIX/lib64")
-
 # Read spack dependencies from the path environment variable
 IFS=':' read -ra deps <<< "$SPACK_DEPENDENCIES"
 for dep in "${deps[@]}"; do
     # Append include directories
+    case "$mode" in
+        cpp|cc|as|ccld)
             if [[ -d $dep/include ]]; then
-        if [[ $mode == cpp || $mode == cc || $mode == as || $mode == ccld ]]; then
                 includes=("${includes[@]}" "$dep/include")
             fi
-    fi
+            ;;
+    esac
 
-    # Append lib and RPATH directories
+    # Append lib/lib64 and RPATH directories
+    case "$mode" in
+        ld|ccld)
             if [[ -d $dep/lib ]]; then
                 if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
                     $add_rpaths && rpaths=("${rpaths[@]}" "$dep/lib")
@@ -376,7 +389,6 @@ for dep in "${deps[@]}"; do
                 fi
             fi
 
-    # Append lib64 and RPATH directories
             if [[ -d $dep/lib64 ]]; then
                 if [[ $SPACK_RPATH_DEPS == *$dep* ]]; then
                     $add_rpaths && rpaths+=("$dep/lib64")
@@ -385,21 +397,24 @@ for dep in "${deps[@]}"; do
                     libdirs+=("$dep/lib64")
                 fi
             fi
+            ;;
+    esac
 done
 
-# Set extra RPATHs
-IFS=':' read -ra extra_rpaths <<< "$SPACK_COMPILER_EXTRA_RPATHS"
-for extra_rpath in "${extra_rpaths[@]}"; do 
-    $add_rpaths && rpaths+=("$extra_rpath")
-    libdirs+=("$extra_rpath")
-done
-
-# Add SPACK_LDLIBS to args
 case "$mode" in
     ld|ccld)
+        # Set extra RPATHs
+        IFS=':' read -ra extra_rpaths <<< "$SPACK_COMPILER_EXTRA_RPATHS"
+        for extra_rpath in "${extra_rpaths[@]}"; do
+            $add_rpaths && rpaths+=("$extra_rpath")
+            libdirs+=("$extra_rpath")
+        done
+
+        # Add SPACK_LDLIBS to args
         for lib in ${SPACK_LDLIBS[@]}; do
             libs+=("${lib#-l}")
         done
+        ;;
 esac
 
 # Filter system locations to the end of each sublist of args
@@ -419,13 +434,18 @@ for sd in ${SPACK_SYSTEM_DIRS[@]}; do
     fi
 done
 
-# Put the arguments together into one list
+# Put the arguments back together in one list
-# Includes come first, then other args, library dirs, and rpaths
+# Includes first
-# rpaths get appropriate flag for ld vs ccld mode
+for dir in "${includes[@]}";  do
-for dir in "${includes[@]}";  do args+=("-I$dir"); done
+    args+=("-I$dir");
-args+=("${other_args[@]}")
+done
-for dir in "${libdirs[@]}"; do args+=("-L$dir"); done
+
-for lib in "${libs[@]}"; do args+=("-l$lib"); done
+# Library search paths
+for dir in "${libdirs[@]}"; do
+    args+=("-L$dir");
+done
+
+# RPATHs arguments
 if [ "$mode" = ccld ]; then
     for dir in "${rpaths[@]}"; do
         args+=("$rpath$dir")
@@ -436,10 +456,18 @@ elif [ "$mode" = ld ]; then
     done
 fi
 
+# Other arguments from the input command
+args+=("${other_args[@]}")
+
+# Inject SPACK_LDLIBS, if supplied
+for lib in "${libs[@]}"; do
+    args+=("-l$lib");
+done
+
 full_command=("$command")
 full_command+=("${args[@]}")
 
-# In test command mode, write out full command for Spack tests.
+# dump the full command if the caller supplies SPACK_TEST_COMMAND=dump-args
 if [[ $SPACK_TEST_COMMAND == dump-args ]]; then
     echo "${full_command[@]}"
     exit