Look into system/local/include and system/local/lib too

Now one can do:

emconfigure ./configure --prefix=/path/to/emscripten/local

And then make install to there, like a real /usr/local.  No
manual bitcode moving.

Now if there  was a way to change default prefix of configure
using an env var...

emcc

@@ -542,7 +542,8 @@ try:
 
   input_files = []
   has_source_inputs = False
-  lib_dirs = [shared.path_from_root('system', 'lib')]
+  lib_dirs = [shared.path_from_root('system', 'local', 'lib'),
+              shared.path_from_root('system', 'lib')]
   libs = []
   for i in range(len(newargs)): # find input files XXX this a simple heuristic. we should really analyze based on a full understanding of gcc params,
                                 # right now we just assume that what is left contains no more |-x OPT| things

tools/shared.py

@@ -200,6 +200,7 @@ if USE_EMSDK:
   # allows projects to override them)
   # Note that -nostdinc++ is not needed, since -nostdinc implies that!
   EMSDK_OPTS = ['-nostdinc', '-Xclang', '-nobuiltininc', '-Xclang', '-nostdsysteminc',
+    '-Xclang', '-isystem' + path_from_root('system', 'local', 'include'),
     '-Xclang', '-isystem' + path_from_root('system', 'include'),
     '-Xclang', '-isystem' + path_from_root('system', 'include', 'emscripten'),
     '-Xclang', '-isystem' + path_from_root('system', 'include', 'bsd'), # posix stuff