diff --git a/browser/installer/package-manifest.in b/browser/installer/package-manifest.in
index 99fee0054b94..bf78ca9fdeed 100644
--- a/browser/installer/package-manifest.in
+++ b/browser/installer/package-manifest.in
@@ -503,9 +503,6 @@
 #ifdef MOZ_SERVICES_SYNC
 @BINPATH@/@PREF_DIR@/services-sync.js
 #endif
-#ifdef MOZ_WEBAPP_RUNTIME
-@BINPATH@/@PREF_DIR@/webapprt@mozilla.org/prefs.js
-#endif
 @BINPATH@/greprefs.js
 @BINPATH@/defaults/autoconfig/platform.js
 @BINPATH@/defaults/autoconfig/prefcalls.js
@@ -629,12 +626,15 @@ bin/components/@DLL_PREFIX@nkgnomevfs@DLL_SUFFIX@
 #endif
 
 #ifdef MOZ_WEBAPP_RUNTIME
-; [Webapp Runtime]
+[WebappRuntime]
 @BINPATH@/webapprt-stub@BIN_SUFFIX@
-@BINPATH@/chrome/webapprt@JAREXT@
-@BINPATH@/chrome/webapprt.manifest
-@BINPATH@/components/WebappRTComponents.manifest
-@BINPATH@/components/WebappRTDirectoryProvider.js
-@BINPATH@/components/WebappRTCommandLineHandler.js
-@BINPATH@/webapprt.ini
+@BINPATH@/webapprt/application.ini
+@BINPATH@/webapprt/chrome.manifest
+@BINPATH@/webapprt/chrome/webapprt@JAREXT@
+@BINPATH@/webapprt/chrome/webapprt.manifest
+@BINPATH@/webapprt/components/CommandLineHandler.js
+@BINPATH@/webapprt/components/DirectoryProvider.js
+@BINPATH@/webapprt/components/components.manifest
+@BINPATH@/webapprt/defaults/preferences/prefs.js
+@BINPATH@/webapprt/modules/WebappRT.jsm
 #endif
diff --git a/browser/locales/Makefile.in b/browser/locales/Makefile.in
index aea19d407ce6..c5a09d26bff3 100644
--- a/browser/locales/Makefile.in
+++ b/browser/locales/Makefile.in
@@ -211,7 +211,7 @@ endif
 clobber-zip:
 	$(RM) $(STAGEDIST)/chrome/$(AB_CD).jar \
 	  $(STAGEDIST)/chrome/$(AB_CD).manifest \
-	  $(STAGEDIST)/defaults/pref/firefox-l10n.js
+	  $(STAGEDIST)/$(PREF_DIR)/firefox-l10n.js
 	$(RM) -rf  $(STAGEDIST)/searchplugins \
 	  $(STAGEDIST)/dictionaries \
 	  $(STAGEDIST)/hyphenation \
diff --git a/config/rules.mk b/config/rules.mk
index 2458e0eaf253..c52223500a74 100644
--- a/config/rules.mk
+++ b/config/rules.mk
@@ -1371,7 +1371,7 @@ $(foreach namespace,$(EXPORTS_NAMESPACES),$(eval $(EXPORT_NAMESPACE_RULE)))
 ifdef GRE_MODULE
 PREF_DIR = greprefs
 else
-ifneq (,$(XPI_NAME)$(LIBXUL_SDK))
+ifneq (,$(XPI_NAME)$(LIBXUL_SDK)$(MOZ_PHOENIX))
 PREF_DIR = defaults/preferences
 else
 PREF_DIR = defaults/pref
diff --git a/js/src/config/rules.mk b/js/src/config/rules.mk
index 2458e0eaf253..c52223500a74 100644
--- a/js/src/config/rules.mk
+++ b/js/src/config/rules.mk
@@ -1371,7 +1371,7 @@ $(foreach namespace,$(EXPORTS_NAMESPACES),$(eval $(EXPORT_NAMESPACE_RULE)))
 ifdef GRE_MODULE
 PREF_DIR = greprefs
 else
-ifneq (,$(XPI_NAME)$(LIBXUL_SDK))
+ifneq (,$(XPI_NAME)$(LIBXUL_SDK)$(MOZ_PHOENIX))
 PREF_DIR = defaults/preferences
 else
 PREF_DIR = defaults/pref
diff --git a/modules/libpref/src/Preferences.cpp b/modules/libpref/src/Preferences.cpp
index 2d0d1093ecad..00742a883832 100644
--- a/modules/libpref/src/Preferences.cpp
+++ b/modules/libpref/src/Preferences.cpp
@@ -43,7 +43,6 @@
 #include "mozilla/HashFunctions.h"
 
 #include "nsXULAppAPI.h"
-#include "nsIXULAppInfo.h"
 
 #include "mozilla/Preferences.h"
 #include "nsAppDirectoryServiceDefs.h"
@@ -85,8 +84,6 @@ namespace mozilla {
 #define INITIAL_PREF_FILES 10
 static NS_DEFINE_CID(kZipReaderCID, NS_ZIPREADER_CID);
 
-#define WEBAPPRT_APPID "webapprt@mozilla.org"
-
 // Prototypes
 static nsresult openPrefFile(nsIFile* aFile);
 static nsresult pref_InitInitialObjects(void);
@@ -861,7 +858,7 @@ pref_LoadPrefsInDir(nsIFile* aDir, char const *const *aSpecialFiles, PRUint32 aS
   if (NS_FAILED(rv)) {
     // If the directory doesn't exist, then we have no reason to complain.  We
     // loaded everything (and nothing) successfully.
-    if (rv == NS_ERROR_FILE_NOT_FOUND)
+    if (rv == NS_ERROR_FILE_NOT_FOUND || rv == NS_ERROR_FILE_TARGET_DOES_NOT_EXIST)
       rv = NS_OK;
     return rv;
   }
@@ -1018,14 +1015,10 @@ static nsresult pref_InitInitialObjects()
   // - $app/defaults/preferences/*.js
   // and in non omni.jar case:
   // - $app/defaults/preferences/*.js
-  //
-  // When we're running WebappRT (i.e. $app == WEBAPPRT_APPID), in omni.jar
-  // case, we also load:
-  // - jar:$gre/omni.jar!/defaults/pref/$WEBAPPRT_APPID/*.js
-  // This allows WebappRT-specific prefs to override those of another app
-  // with whom it shares an app dir (i.e. Firefox).
-  // (A $WEBAPPRT_APPID dir is similarly hardcoded into the app pref dir list
-  // in nsXREDirProvider for when we're running WebappRT in non omni.jar case.)
+  // When $app == $gre, we additionally load, in omni.jar case:
+  // - jar:$gre/omni.jar!/defaults/preferences/*.js
+  // Thus, in omni.jar case, we always load app-specific default preferences
+  // from omni.jar, whether or not $app == $gre.
 
   nsZipFind *findPtr;
   nsAutoPtr<nsZipFind> find;
@@ -1049,30 +1042,6 @@ static nsresult pref_InitInitialObjects()
     }
 
     prefEntries.Sort();
-
-    // Load jar:$gre/omni.jar!/defaults/pref/$WEBAPPRT_APPID/*.js
-    // if we're running WebappRT.
-    nsCOMPtr<nsIXULAppInfo> appInfo =
-      do_GetService("@mozilla.org/xre/app-info;1", &rv);
-    if (NS_SUCCEEDED(rv)) {
-      nsCAutoString appID;
-      if (NS_SUCCEEDED(appInfo->GetID(appID)) && appID.Equals(WEBAPPRT_APPID)) {
-        nsCAutoString prefsPath("defaults/pref/");
-        prefsPath.Append(appID);
-        prefsPath.AppendLiteral("/*.js$");
-        rv = jarReader->FindInit(prefsPath.get(), &findPtr);
-        NS_ENSURE_SUCCESS(rv, rv);
-
-        // Make sure the files get read last by putting them at the beginning
-        // of the list of pref entries (which is processed backwards), so prefs
-        // in these app-specific files override those in non-app-specific ones.
-        find = findPtr;
-        while (NS_SUCCEEDED(find->FindNext(&entryName, &entryNameLen))) {
-          prefEntries.InsertElementAt(0, Substring(entryName, entryNameLen));
-        }
-      }
-    }
-
     for (PRUint32 i = prefEntries.Length(); i--; ) {
       rv = pref_ReadPrefFromJar(jarReader, prefEntries[i].get());
       if (NS_FAILED(rv))
@@ -1123,7 +1092,12 @@ static nsresult pref_InitInitialObjects()
     NS_WARNING("Error parsing application default preferences.");
 
   // Load jar:$app/omni.jar!/defaults/preferences/*.js
+  // or jar:$gre/omni.jar!/defaults/preferences/*.js.
   nsRefPtr<nsZipArchive> appJarReader = mozilla::Omnijar::GetReader(mozilla::Omnijar::APP);
+  // GetReader(mozilla::Omnijar::APP) returns null when $app == $gre, in which
+  // case we look for app-specific default preferences in $gre.
+  if (!appJarReader)
+    appJarReader = mozilla::Omnijar::GetReader(mozilla::Omnijar::GRE);
   if (appJarReader) {
     rv = appJarReader->FindInit("defaults/preferences/*.js$", &findPtr);
     NS_ENSURE_SUCCESS(rv, rv);
diff --git a/toolkit/locales/l10n.mk b/toolkit/locales/l10n.mk
index c70e07012fe2..2409c0865421 100644
--- a/toolkit/locales/l10n.mk
+++ b/toolkit/locales/l10n.mk
@@ -172,6 +172,9 @@ endif
 endif
 ifdef MOZ_OMNIJAR
 	@(cd $(STAGEDIST) && $(UNPACK_OMNIJAR))
+ifdef MOZ_WEBAPP_RUNTIME
+	@(cd $(STAGEDIST)/webapprt && $(UNPACK_OMNIJAR_WEBAPP_RUNTIME))
+endif
 endif
 	$(MAKE) clobber-zip AB_CD=$(AB_CD)
 	$(NSINSTALL) -D $(DIST)/$(PKG_PATH)
diff --git a/toolkit/mozapps/installer/Packager.pm b/toolkit/mozapps/installer/Packager.pm
index 7d47816e90bf..cdf2a170cc62 100644
--- a/toolkit/mozapps/installer/Packager.pm
+++ b/toolkit/mozapps/installer/Packager.pm
@@ -234,7 +234,10 @@ sub do_copyfile
 
   # set the destination path, if alternate destination given, use it.
   if ($flat) {
-    if ($srcsuffix eq ".manifest" && $srcpath =~ m'/(chrome|components)/$') {
+    # WebappRuntime has manifests that shouldn't be flattened, even though it
+    # gets packaged with Firefox, which does get flattened, so special-case it.
+    if ($srcsuffix eq ".manifest" && $srcpath =~ m'/(chrome|components)/$' &&
+        $component ne "WebappRuntime") {
       my $subdir = $1;
       if ($component eq "") {
         die ("Manifest file was not part of a component.");
diff --git a/toolkit/mozapps/installer/packager.mk b/toolkit/mozapps/installer/packager.mk
index 9603302fab46..414a87c375bf 100644
--- a/toolkit/mozapps/installer/packager.mk
+++ b/toolkit/mozapps/installer/packager.mk
@@ -547,13 +547,34 @@ UNPACK_OMNIJAR	= \
     mv tmp.manifest $$m; \
   done
 
+ifdef MOZ_WEBAPP_RUNTIME
+# It's simpler to pack the webapp runtime, because it doesn't have any
+# binary components.  We also don't pre-generate the startup cache, which seems
+# unnecessary, given the small size of the runtime, although it might become
+# more valuable over time.
+PACK_OMNIJAR_WEBAPP_RUNTIME	= \
+  rm -f $(OMNIJAR_NAME); \
+  $(ZIP) -r9m $(OMNIJAR_NAME) $(OMNIJAR_FILES) -x $(NON_OMNIJAR_FILES) && \
+  $(OPTIMIZE_JARS_CMD) --optimize $(JARLOG_DIR_AB_CD) ./ ./
+UNPACK_OMNIJAR_WEBAPP_RUNTIME	= \
+  $(OPTIMIZE_JARS_CMD) --deoptimize $(JARLOG_DIR_AB_CD) ./ ./ && \
+  $(UNZIP) -o $(OMNIJAR_NAME)
+
+PREPARE_PACKAGE	= (cd $(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH) && $(PACK_OMNIJAR)) && \
+	              (cd $(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH)/webapprt && $(PACK_OMNIJAR_WEBAPP_RUNTIME)) && \
+	              (cd $(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH) && $(CREATE_PRECOMPLETE_CMD))
+UNMAKE_PACKAGE	= $(INNER_UNMAKE_PACKAGE) && \
+	              (cd $(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH) && $(UNPACK_OMNIJAR)) && \
+	              (cd $(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH)/webapprt && $(UNPACK_OMNIJAR_WEBAPP_RUNTIME))
+else # ndef MOZ_WEBAPP_RUNTIME
 PREPARE_PACKAGE	= (cd $(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH) && $(PACK_OMNIJAR)) && \
 	              (cd $(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH) && $(CREATE_PRECOMPLETE_CMD))
 UNMAKE_PACKAGE	= $(INNER_UNMAKE_PACKAGE) && (cd $(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH) && $(UNPACK_OMNIJAR))
-else
+endif # def MOZ_WEBAPP_RUNTIME
+else # ndef MOZ_OMNIJAR
 PREPARE_PACKAGE	= (cd $(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH) && $(CREATE_PRECOMPLETE_CMD))
 UNMAKE_PACKAGE	= $(INNER_UNMAKE_PACKAGE)
-endif
+endif # def MOZ_OMNIJAR
 
 ifdef MOZ_INTERNAL_SIGNING_FORMAT
 MOZ_SIGN_PREPARED_PACKAGE_CMD=$(MOZ_SIGN_CMD) $(foreach f,$(MOZ_INTERNAL_SIGNING_FORMAT),-f $(f)) $(foreach i,$(SIGN_INCLUDES),-i $(i)) $(foreach x,$(SIGN_EXCLUDES),-x $(x)) --nsscmd "$(SIGN_CMD)"
@@ -720,6 +741,9 @@ endif
 	@$(NSINSTALL) -D $(DEPTH)/installer-stage/core
 ifdef MOZ_OMNIJAR
 	@(cd $(DIST)/$(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH) && $(PACK_OMNIJAR))
+ifdef MOZ_WEBAPP_RUNTIME
+	@(cd $(DIST)/$(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH)/webapprt && $(PACK_OMNIJAR_WEBAPP_RUNTIME))
+endif
 endif
 	@cp -av $(DIST)/$(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH)/. $(DEPTH)/installer-stage/core
 	@(cd $(DEPTH)/installer-stage/core && $(CREATE_PRECOMPLETE_CMD))
@@ -873,6 +897,9 @@ ifeq (bundle,$(MOZ_FS_LAYOUT))
 endif
 ifdef MOZ_OMNIJAR
 	cd $(DIST)/$(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH) && $(PACK_OMNIJAR)
+ifdef MOZ_WEBAPP_RUNTIME
+	cd $(DIST)/$(STAGEPATH)$(MOZ_PKG_DIR)$(_BINPATH)/webapprt && $(PACK_OMNIJAR_WEBAPP_RUNTIME))
+endif
 endif
 	$(NSINSTALL) -D $(DESTDIR)$(installdir)
 	(cd $(DIST)/$(MOZ_PKG_DIR) && tar $(TAR_CREATE_FLAGS) - .) | \
diff --git a/toolkit/mozapps/installer/windows/nsis/makensis.mk b/toolkit/mozapps/installer/windows/nsis/makensis.mk
index 05d298d70f49..9278aa39e197 100644
--- a/toolkit/mozapps/installer/windows/nsis/makensis.mk
+++ b/toolkit/mozapps/installer/windows/nsis/makensis.mk
@@ -113,6 +113,6 @@ webapp_uninstaller::
 	$(INSTALL) $(addprefix $(MOZILLA_DIR)/toolkit/mozapps/installer/windows/nsis/,$(TOOLKIT_NSIS_FILES)) $(CONFIG_DIR)
 	$(INSTALL) $(addprefix $(MOZILLA_DIR)/other-licenses/nsis/Plugins/,$(CUSTOM_NSIS_PLUGINS)) $(CONFIG_DIR)
 	cd $(CONFIG_DIR) && $(MAKENSISU) webapp-uninstaller.nsi
-	$(NSINSTALL) -D $(DIST)/bin/
-	cp $(CONFIG_DIR)/webapp-uninstaller.exe $(DIST)/bin
+	$(NSINSTALL) -D $(FINAL_TARGET)
+	cp $(CONFIG_DIR)/webapp-uninstaller.exe $(FINAL_TARGET)
 endif
diff --git a/toolkit/xre/nsXREDirProvider.cpp b/toolkit/xre/nsXREDirProvider.cpp
index 15fca16ffa1a..ecbcc0d2e0b5 100644
--- a/toolkit/xre/nsXREDirProvider.cpp
+++ b/toolkit/xre/nsXREDirProvider.cpp
@@ -99,8 +99,6 @@
 
 #define PREF_OVERRIDE_DIRNAME "preferences"
 
-#define WEBAPPRT_APPID "webapprt@mozilla.org"
-
 static already_AddRefed<nsILocalFile>
 CloneAndAppend(nsIFile* aFile, const char* name)
 {
@@ -650,13 +648,6 @@ nsXREDirProvider::GetFilesInternal(const char* aProperty,
     LoadDirsIntoArray(mAppBundleDirectories,
                       kAppendPrefDir, directories);
 
-    // Include the WebappRT-specific prefs dir if we're running WebappRT.
-    if (gAppData && !strcmp(gAppData->ID, WEBAPPRT_APPID)) {
-      const char *const kAppendAppIDPrefDir[] =
-        { "defaults", "pref", gAppData->ID, nsnull };
-      LoadDirIntoArray(mXULAppDir, kAppendAppIDPrefDir, directories);
-    }
-
     rv = NS_NewArrayEnumerator(aResult, directories);
   }
   else if (!strcmp(aProperty, NS_EXT_PREFS_DEFAULTS_DIR_LIST)) {
diff --git a/webapprt/WebappRTCommandLineHandler.js b/webapprt/CommandLineHandler.js
similarity index 100%
rename from webapprt/WebappRTCommandLineHandler.js
rename to webapprt/CommandLineHandler.js
diff --git a/webapprt/WebappRTDirectoryProvider.js b/webapprt/DirectoryProvider.js
similarity index 96%
rename from webapprt/WebappRTDirectoryProvider.js
rename to webapprt/DirectoryProvider.js
index 08f857ab7b1a..53dd1d9560c1 100644
--- a/webapprt/WebappRTDirectoryProvider.js
+++ b/webapprt/DirectoryProvider.js
@@ -11,7 +11,7 @@ const NS_APP_CHROME_DIR_LIST = "AChromDL";
 
 Cu.import("resource://gre/modules/FileUtils.jsm");
 Cu.import("resource://gre/modules/XPCOMUtils.jsm");
-Cu.import("resource://gre/modules/WebappRT.jsm");
+Cu.import("resource://webapprt/modules/WebappRT.jsm");
 
 function DirectoryProvider() {}
 
diff --git a/webapprt/Makefile.in b/webapprt/Makefile.in
index bbc6e8f4cb6c..00b3fcc5e4ac 100644
--- a/webapprt/Makefile.in
+++ b/webapprt/Makefile.in
@@ -9,6 +9,10 @@ VPATH     = @srcdir@
 
 include $(topsrcdir)/config/config.mk
 
+# config.mk sets FINAL_TARGET to $(DIST)/bin, but we want to copy build products
+# into a WebappRT-specific subdirectory, so we redefine it here.
+FINAL_TARGET = $(DIST)/bin/webapprt
+
 DIRS = $(NULL)
 
 ifneq (,$(filter WINNT,$(OS_ARCH)))
@@ -20,29 +24,32 @@ endif # mac
 endif # windows
 
 EXTRA_PP_COMPONENTS = \
-  WebappRTComponents.manifest \
-  WebappRTCommandLineHandler.js \
-  WebappRTDirectoryProvider.js \
+  components.manifest \
+  CommandLineHandler.js \
+  DirectoryProvider.js \
   $(NULL)
 
 EXTRA_JS_MODULES = \
-	WebappRT.jsm \
-	$(NULL)
+  WebappRT.jsm \
+  $(NULL)
 
 include $(topsrcdir)/config/rules.mk
 
+libs::
+	$(PYTHON) $(MOZILLA_DIR)/config/buildlist.py $(FINAL_TARGET)/chrome.manifest "resource webapprt ./"
+
 libs:: prefs.js
-	$(NSINSTALL) -D $(DIST)/bin/defaults/pref/webapprt@mozilla.org
-	$(INSTALL) $^ $(DIST)/bin/defaults/pref/webapprt@mozilla.org
+	$(NSINSTALL) -D $(FINAL_TARGET)/defaults/preferences
+	$(INSTALL) $^ $(FINAL_TARGET)/defaults/preferences
 
 GRE_MILESTONE := $(shell tail -n 1 $(topsrcdir)/config/milestone.txt 2>/dev/null || tail -1 $(topsrcdir)/config/milestone.txt)
 GRE_BUILDID := $(shell cat $(DEPTH)/config/buildid)
 DEFINES += -DGRE_MILESTONE=$(GRE_MILESTONE) -DGRE_BUILDID=$(GRE_BUILDID)
 
-webapprt.ini: webapprt.ini.in $(DEPTH)/config/buildid $(topsrcdir)/config/milestone.txt
+application.ini: application.ini.in $(DEPTH)/config/buildid $(topsrcdir)/config/milestone.txt
 	$(PYTHON) $(topsrcdir)/config/Preprocessor.py $(DEFINES) $< > $@
 
-libs:: webapprt.ini
-	$(INSTALL) webapprt.ini $(DIST)/bin
+libs:: application.ini
+	$(INSTALL) application.ini $(FINAL_TARGET)
 
-GARBAGE += webapprt.ini
+GARBAGE += application.ini
diff --git a/webapprt/webapprt.ini.in b/webapprt/application.ini.in
similarity index 100%
rename from webapprt/webapprt.ini.in
rename to webapprt/application.ini.in
diff --git a/webapprt/WebappRTComponents.manifest b/webapprt/components.manifest
similarity index 62%
rename from webapprt/WebappRTComponents.manifest
rename to webapprt/components.manifest
index ad76433432b4..f33ef7f8b4e8 100644
--- a/webapprt/WebappRTComponents.manifest
+++ b/webapprt/components.manifest
@@ -1,9 +1,9 @@
-# WebappRTCommandLineHandler.js
-component {6d69c782-40a3-469b-8bfd-3ee366105a4a} WebappRTCommandLineHandler.js application=webapprt@mozilla.org
+# CommandLineHandler.js
+component {6d69c782-40a3-469b-8bfd-3ee366105a4a} CommandLineHandler.js application=webapprt@mozilla.org
 contract @mozilla.org/webapprt/clh;1 {6d69c782-40a3-469b-8bfd-3ee366105a4a} application=webapprt@mozilla.org
 category command-line-handler x-default @mozilla.org/webapprt/clh;1 application=webapprt@mozilla.org
 
-# WebappRTDirectoryProvider.js
-component {e1799fda-4b2f-4457-b671-e0641d95698d} WebappRTDirectoryProvider.js application=webapprt@mozilla.org
+# DirectoryProvider.js
+component {e1799fda-4b2f-4457-b671-e0641d95698d} DirectoryProvider.js application=webapprt@mozilla.org
 contract @mozilla.org/webapprt/directory-provider;1 {e1799fda-4b2f-4457-b671-e0641d95698d} application=webapprt@mozilla.org
 category xpcom-directory-providers webapprt-directory-provider @mozilla.org/webapprt/directory-provider;1 application=webapprt@mozilla.org
diff --git a/webapprt/content/webapp.js b/webapprt/content/webapp.js
index 2f8fbe3363d4..f7b5afe53de9 100644
--- a/webapprt/content/webapp.js
+++ b/webapprt/content/webapp.js
@@ -6,7 +6,7 @@ const Cc = Components.classes;
 const Ci = Components.interfaces;
 const Cu = Components.utils;
 
-Cu.import("resource://gre/modules/WebappRT.jsm");
+Cu.import("resource://webapprt/modules/WebappRT.jsm");
 Cu.import("resource://gre/modules/Services.jsm");
 
 function onLoad() {
diff --git a/webapprt/jar.mn b/webapprt/jar.mn
index f64f668cb753..1874c89ae79f 100644
--- a/webapprt/jar.mn
+++ b/webapprt/jar.mn
@@ -1,4 +1,4 @@
 webapprt.jar:
-%  content webapprt %content/
-*       content/webapp.js                         (content/webapp.js)
-*       content/webapp.xul                        (content/webapp.xul)
+% content webapprt %content/
+* content/webapp.js                     (content/webapp.js)
+* content/webapp.xul                    (content/webapp.xul)
diff --git a/webapprt/mac/webapprt.mm b/webapprt/mac/webapprt.mm
index 3d6da1b6aeae..f48d5ca64c41 100644
--- a/webapprt/mac/webapprt.mm
+++ b/webapprt/mac/webapprt.mm
@@ -32,11 +32,14 @@
 const char WEBAPPRT_EXECUTABLE[] = "webapprt-stub";
 const char FXAPPINI_NAME[] = "application.ini";
 const char WEBAPPINI_NAME[] = "webapp.ini";
-const char WEBRTINI_NAME[] = "webapprt.ini";
+const char WEBRTINI_NAME[] = "application.ini";
 
 //need the correct relative path here
 const char APP_CONTENTS_PATH[] = "/Contents/MacOS/";
 
+//the path to the WebappRT subdir within the Firefox app contents dir
+const char WEBAPPRT_PATH[] = "webapprt/";
+
 void ExecNewBinary(NSString* launchPath);
 
 NSString *PathToWebRT(NSString* alternateBinaryID);
@@ -212,10 +215,14 @@ main(int argc, char **argv)
           @throw MakeException(@"Error", @"Unable to parse environment files for application startup");
         }
 
-        // Get the path to the runtime's INI file.  This should be in the
-        // same directory as the GRE.
-        snprintf(rtINIPath, MAXPATHLEN, "%s%s%s", [firefoxPath UTF8String], APP_CONTENTS_PATH, WEBRTINI_NAME);
-        NSLog(@"webapprt.ini path: %s", rtINIPath);
+        // Get the path to the runtime directory.
+        char rtDir[MAXPATHLEN];
+        snprintf(rtDir, MAXPATHLEN, "%s%s%s", [firefoxPath UTF8String], APP_CONTENTS_PATH, WEBAPPRT_PATH);
+
+        // Get the path to the runtime's INI file.  This is in the runtime
+        // directory.
+        snprintf(rtINIPath, MAXPATHLEN, "%s%s%s%s", [firefoxPath UTF8String], APP_CONTENTS_PATH, WEBAPPRT_PATH, WEBRTINI_NAME);
+        NSLog(@"WebappRT application.ini path: %s", rtINIPath);
         if (![[NSFileManager defaultManager] fileExistsAtPath:[NSString stringWithFormat:@"%s", rtINIPath]]) {
           NSString* msg = [NSString stringWithFormat: @"This copy of Firefox (%@) cannot run web applications, because it is missing important files", firefoxVersion];
           @throw MakeException(@"Missing WebRT Files", msg);
@@ -229,13 +236,13 @@ main(int argc, char **argv)
         }
 
         if (!rtINI) {
-          NSLog(@"Error: missing webapprt.ini");
+          NSLog(@"Error: missing WebappRT application.ini");
           @throw MakeException(@"Error", @"Missing base INI file.");
         }
 
         nsXREAppData *webShellAppData;
         if (NS_FAILED(XRE_CreateAppData(rtINI, &webShellAppData))) {
-          NSLog(@"Couldn't read webapprt.ini: %s", rtINIPath);
+          NSLog(@"Couldn't read WebappRT application.ini: %s", rtINIPath);
           @throw MakeException(@"Error", @"Unable to parse base INI file.");
         }
 
@@ -248,7 +255,7 @@ main(int argc, char **argv)
         SetAllocatedString(webShellAppData->profile, profile);
 
         nsCOMPtr<nsILocalFile> directory;
-        if (NS_FAILED(XRE_GetFileFromPath(greDir, getter_AddRefs(directory)))) {
+        if (NS_FAILED(XRE_GetFileFromPath(rtDir, getter_AddRefs(directory)))) {
           NSLog(@"Unable to open app dir");
           @throw MakeException(@"Error", @"Unable to open application directory.");
         }
diff --git a/webapprt/prefs.js b/webapprt/prefs.js
index e828e05481ed..00ea70414a09 100644
--- a/webapprt/prefs.js
+++ b/webapprt/prefs.js
@@ -3,11 +3,3 @@
  * You can obtain one at http://mozilla.org/MPL/2.0/. */
 
 pref("browser.chromeURL", "chrome://webapprt/content/webapp.xul");
-
-// We set this to the value of DEFAULT_HIDDENWINDOW_URL in nsAppShellService.cpp
-// so our app is treated as not having an application-provided hidden window.
-// Ideally, we could just leave it out, but because we are being distributed
-// in a unified directory with Firefox, Firefox's preferences are being read
-// before ours, which means this preference is being set by Firefox, and we need
-// to set it here to override the Firefox-provided value.
-pref("browser.hiddenWindowChromeURL", "resource://gre-resources/hiddenWindow.html");
diff --git a/webapprt/win/Makefile.in b/webapprt/win/Makefile.in
index e3ad2b4ef26d..8f0cc0e4faea 100644
--- a/webapprt/win/Makefile.in
+++ b/webapprt/win/Makefile.in
@@ -7,7 +7,7 @@ topsrcdir = @top_srcdir@
 srcdir    = @srcdir@
 VPATH     = @srcdir@
 
-include $(DEPTH)/config/autoconf.mk
+include $(topsrcdir)/config/config.mk
 
 # Build a binary bootstrapping with XRE_main
 PROGRAM   = webapprt-stub$(BIN_SUFFIX)
@@ -51,8 +51,6 @@ SFX_MODULE = $(topsrcdir)/other-licenses/7zstub/firefox/7zSD.sfx
 APP_VERSION := $(shell cat $(topsrcdir)/browser/config/version.txt)
 DEFINES += -DAPP_VERSION=$(APP_VERSION)
 
-include $(topsrcdir)/config/config.mk
-
 ifdef _MSC_VER
 # Always enter a Windows program through wmain, whether or not we're
 # a console application.
diff --git a/webapprt/win/webapprt.cpp b/webapprt/win/webapprt.cpp
index 44f6d115f98b..93c4402de42f 100644
--- a/webapprt/win/webapprt.cpp
+++ b/webapprt/win/webapprt.cpp
@@ -27,7 +27,7 @@ XRE_mainType XRE_main;
 namespace {
   const char kAPP_INI[] = "application.ini";
   const char kWEBAPP_INI[] = "webapp.ini";
-  const char kWEBAPPRT_INI[] = "webapprt.ini";
+  const char kWEBAPPRT_PATH[] = "webapprt";
   const char kAPP_ENV_PREFIX[] = "XUL_APP_FILE=";
   const char kAPP_RT[] = "webapprt-stub.exe";
 
@@ -262,10 +262,14 @@ namespace {
 
       ScopedLogging log;
 
-      // Get the path to the runtime's INI file.  This should be in the
-      // same directory as the GRE.
+      // Get the path to the runtime.
+      char rtPath[MAXPATHLEN];
+      rv = joinPath(rtPath, greDir, kWEBAPPRT_PATH, MAXPATHLEN);
+      NS_ENSURE_SUCCESS(rv, rv);
+
+      // Get the path to the runtime's INI file.
       char rtIniPath[MAXPATHLEN];
-      rv = joinPath(rtIniPath, greDir, kWEBAPPRT_INI, MAXPATHLEN);
+      rv = joinPath(rtIniPath, rtPath, kAPP_INI, MAXPATHLEN);
       NS_ENSURE_SUCCESS(rv, false);
 
       // Load the runtime's INI from its path.
@@ -284,13 +288,11 @@ namespace {
       SetAllocatedString(webShellAppData->profile, profile);
 
       nsCOMPtr<nsILocalFile> directory;
-      rv = XRE_GetFileFromPath(greDir,
-                               getter_AddRefs(directory));
+      rv = XRE_GetFileFromPath(rtPath, getter_AddRefs(directory));
       NS_ENSURE_SUCCESS(rv, false);
 
       nsCOMPtr<nsILocalFile> xreDir;
-      rv = XRE_GetFileFromPath(greDir,
-                               getter_AddRefs(xreDir));
+      rv = XRE_GetFileFromPath(greDir, getter_AddRefs(xreDir));
       NS_ENSURE_SUCCESS(rv, false);
 
       xreDir.forget(&webShellAppData->xreDirectory);
diff --git a/xpfe/appshell/src/nsAppShellService.cpp b/xpfe/appshell/src/nsAppShellService.cpp
index 83a4d4dc8acc..bb91c183a48d 100644
--- a/xpfe/appshell/src/nsAppShellService.cpp
+++ b/xpfe/appshell/src/nsAppShellService.cpp
@@ -121,22 +121,8 @@ nsAppShellService::CreateHiddenWindow()
   PRUint32    chromeMask = 0;
   nsAdoptingCString prefVal =
       Preferences::GetCString("browser.hiddenWindowChromeURL");
-
-  // Set mApplicationProvidedHiddenWindow to true only if there is a hidden
-  // window chrome URL in preferences AND it is set to a non-default value.
-  // This enables an app that doesn't have a hidden window (like WebappRT)
-  // to share an app directory with one that does (like Firefox), the former
-  // taking advantage of this behavior to "unset" the latter's hidden window
-  // pref by setting it to the default value.
-  //
-  // (Ideally, the former would be able to simply unset the latter's pref,
-  // but there is no way to do that; even more ideally, the two apps would not
-  // share an app directory, but in the case of WebappRT and Firefox that's
-  // a longer-term fix.)
-  //
-  mApplicationProvidedHiddenWindow = prefVal.get() && strcmp(prefVal.get(), DEFAULT_HIDDENWINDOW_URL) ? true : false;
-
-  const char* hiddenWindowURL = mApplicationProvidedHiddenWindow ? prefVal.get() : DEFAULT_HIDDENWINDOW_URL;
+  const char* hiddenWindowURL = prefVal.get() ? prefVal.get() : DEFAULT_HIDDENWINDOW_URL;
+  mApplicationProvidedHiddenWindow = prefVal.get() ? true : false;
 #else
   static const char hiddenWindowURL[] = DEFAULT_HIDDENWINDOW_URL;
   PRUint32    chromeMask =  nsIWebBrowserChrome::CHROME_ALL;