There are two problems with the current IntelliJ files.

First, the VCS files have the wrong roots. The file .idea/vcs.xml contains the following:

<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
  <component name="VcsDirectoryMappings">
    <mapping directory="" vcs="" />
    <mapping directory="$PROJECT_DIR$/../../deploy" vcs="hg4idea" />
    <mapping directory="$PROJECT_DIR$" vcs="hg4idea" />
    <mapping directory="$PROJECT_DIR$/../../rt-closed" vcs="hg4idea" />
  </component>
</project>

deploy and rt-closed are on the same level as PROJECT_DIR, so should be defined as:
    <mapping directory="$PROJECT_DIR$/../deploy" vcs="hg4idea" />
    <mapping directory="$PROJECT_DIR$/../rt-closed" vcs="hg4idea" />

Second, opening the project in IntelliJ 13 creates the following diff:

diff -r 8cd285044aad .idea/gradle.xml
--- a/.idea/gradle.xml Mon Jan 06 23:41:14 2014 +0200
+++ b/.idea/gradle.xml Mon Jan 06 23:56:16 2014 +0200
@@ -1,9 +1,3 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
- <component name="GradleSettings">
- <option name="linkedProjectPath" value="" />
- <option name="preferLocalInstallationToWrapper" value="true" />
- <option name="useAutoImport" value="false" />
- </component>
-</project>
+<project version="4" />