Gradel's behavior has changed from 0.8 to 0.9 when it comes to the resolution of runtime dependencies. I've attached a ZIP-file containing a simple example.

The test-case consists of two projects called "project" and "framework". The latter one is a multi-project build with dependencies between its modules:

framework/libA/build.gradle
dependencies {
compile project(':libB')
}

framework/libB/build.gradle
dependencies {
runtime project(':libC')
}

The other project has a module-dependency to libA:

project/build.gradle
dependencies {
compile 'eg.example:libA:1.0.0-SNAPSHOT'
}

With Gradle 0.8 everthing works as expected and running `gradle war` in ./project creates a WAR-file containing all three JARs (libA, libB and libC).

With Gradle 0.9-20100208163629+0100, only libA and libB are present, whereas libC is missing.

This is the command output of the different versions. The difference id that in 8.0 libB is requested with conf=master,compile,runtime, whereas in 9.0 only the compile configuration is requested:

$ gradle -v

------------------------------------------------------------
Gradle 0.8
------------------------------------------------------------

Gradle buildtime: Monday, September 28, 2009 2:01:59 PM CEST
Groovy: 1.6.4
Ant: Apache Ant version 1.7.0 compiled on December 13 2006
Ivy: 2.1.0-rc2
Java: 1.6.0_17
JVM: 14.3-b01-101
JVM Vendor: Apple Inc.
OS Name: Mac OS X

$ gradle --dependencies
:reportTask

------------------------------------------------------------
Root Project
------------------------------------------------------------
archives - Configuration for the default artifacts.
compile - Classpath for compiling the sources.

BUILD SUCCESSFUL

$ gradle -v

------------------------------------------------------------
Gradle 0.9-20100208163629+0100
------------------------------------------------------------

Gradle buildtime: Montag, 8. Februar 2010 16:36 Uhr MEZ
Groovy: 1.7.0
Ant: Apache Ant version 1.7.0 compiled on December 13 2006
Ivy: 2.1.0
Java: 1.6.0_17
JVM: 14.3-b01-101
JVM Vendor: Apple Inc.
OS Name: Mac OS X

$ gradle --dependencies
The Project.usePlugin() method is deprecated and will be removed in the next version of Gradle. You should use the apply() method instead.
:report

------------------------------------------------------------
Root Project
------------------------------------------------------------
archives - Configuration for the default artifacts.
compile - Classpath for compiling the sources.
downloading (790 B) file:/Users/flx/.m2/repository/eg/example/libA/1.0.0-SNAPSHOT/libA-1.0.0-SNAPSHOT.pom
..

BUILD SUCCESSFUL