Sorry for using the "blocker" priority, but I think it may be appropriate here...

I have a project "jee:war" which generates a WAR, with a little extra customization in order to add a WebStart application to the WAR (build file attached). The client-side WebStart dependencies are specified using a custom configuration named "webstart".

Now, in terms of alphabetical order of the sub-projects, the "jee" directory which contains the "war" directory is almost last; there is only one sub-project that is transitively referenced in the "webstart" configuration that comes after "jee", and that is "label-printing". This is the dependency chain for the "label-printing" module which should get included transitively via the encoding client as part of the "webstart" configuration: "encoding:client" > "label-printing:client" > "label-printing:facade".

However, looking at the logs ("gradle jee:war:dependencies -i", output is attached), it appears that the sub-projects are evaluated in alphabetical order, and that the custom "webstart" configuration in "jee:war" is resolved at the time that the "jee:war" project is evaluated – before the "label-printing:client" project is evaluated. It appears that this results in any transitive dependencies out of "label-printing:client" being omitted from the custom "webstart" configuration, because the "label-printing:client" project hasn't been evaluated yet.

So it looks like some transitive project dependencies are being omitted from custom configurations just because they have a name that starts with a letter which appears later in the alphabet! If we rename the "jee:war" module to "xjee:war", so that it's last in the list of sub-projects (alphabetically), the "label-printing:facade" project gets included transitively in the custom "webstart" configuration!

Here's the most relevant section of the log file (with a couple of lines bolded, for emphasis):

Settings evaluated using settings file 'C:\work\trunk\Core\r2\Development\Sources\xbo\settings.gradle'.
Projects loaded. Root project using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\build.gradle'.
Included projects: [root project 'xbo', project ':bootstrap', project ':dsp-adapter', project ':encoding', project ':framework', project ':hardware', project ':jee', project ':label-printing', project ':routing-matrix', project ':sort-programs', project ':bootstrap:client', project ':bootstrap:data-loader', project ':bootstrap:persistence', project ':bootstrap:server', project ':bootstrap:test', project ':dsp-adapter:abol', project ':dsp-adapter:api', project ':dsp-adapter:canada', project ':dsp-adapter:indicia', project ':dsp-adapter:xlogics', project ':encoding:client', project ':encoding:facade', project ':encoding:integration', project ':encoding:legacyimporter', project ':encoding:mock', project ':encoding:server', project ':encoding:shared', project ':framework:client', project ':framework:facade', project ':framework:server', project ':framework:shared', project ':hardware:barcode-scanner', project ':hardware:label-printer', project ':hardware:scale', project ':hardware:scale-calibration', project ':hardware:scale-calibration-mock', project ':hardware:shared', project ':jee:war', project ':label-printing:client', project ':label-printing:facade', project ':label-printing:server', project ':label-printing:shared', project ':routing-matrix:api', project ':routing-matrix:server', project ':routing-matrix:test-bench', project ':sort-programs:api', project ':sort-programs:server']
Evaluating root project 'xbo' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\build.gradle'.
Evaluating project ':bootstrap' using empty build file.
Evaluating project ':dsp-adapter' using empty build file.
Evaluating project ':encoding' using empty build file.
Evaluating project ':framework' using empty build file.
Evaluating project ':hardware' using empty build file.
Evaluating project ':jee' using empty build file.
Evaluating project ':label-printing' using empty build file.
Evaluating project ':routing-matrix' using empty build file.
Evaluating project ':sort-programs' using empty build file.
Evaluating project ':bootstrap:client' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\bootstrap\client\build.gradle'.
Evaluating project ':bootstrap:data-loader' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\bootstrap\data-loader\build.gradle'.
Evaluating project ':bootstrap:persistence' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\bootstrap\persistence\build.gradle'.
Evaluating project ':bootstrap:server' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\bootstrap\server\build.gradle'.
Evaluating project ':bootstrap:test' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\bootstrap\test\build.gradle'.
Evaluating project ':dsp-adapter:abol' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\dsp-adapter\abol\build.gradle'.
Evaluating project ':dsp-adapter:api' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\dsp-adapter\api\build.gradle'.
Evaluating project ':dsp-adapter:canada' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\dsp-adapter\canada\build.gradle'.
Evaluating project ':dsp-adapter:indicia' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\dsp-adapter\indicia\build.gradle'.
Evaluating project ':dsp-adapter:xlogics' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\dsp-adapter\xlogics\build.gradle'.
Evaluating project ':encoding:client' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\encoding\client\build.gradle'.
Evaluating project ':encoding:facade' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\encoding\facade\build.gradle'.
Evaluating project ':encoding:integration' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\encoding\integration\build.gradle'.
Evaluating project ':encoding:legacyimporter' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\encoding\legacyimporter\build.gradle'.
Evaluating project ':encoding:mock' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\encoding\mock\build.gradle'.
Evaluating project ':encoding:server' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\encoding\server\build.gradle'.
Evaluating project ':encoding:shared' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\encoding\shared\build.gradle'.
Evaluating project ':framework:client' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\framework\client\build.gradle'.
Evaluating project ':framework:facade' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\framework\facade\build.gradle'.
Evaluating project ':framework:server' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\framework\server\build.gradle'.
Evaluating project ':framework:shared' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\framework\shared\build.gradle'.
Evaluating project ':hardware:barcode-scanner' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\hardware\barcode-scanner\build.gradle'.
Evaluating project ':hardware:label-printer' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\hardware\label-printer\build.gradle'.
Evaluating project ':hardware:scale' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\hardware\scale\build.gradle'.
Evaluating project ':hardware:scale-calibration' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\hardware\scale-calibration\build.gradle'.
Evaluating project ':hardware:scale-calibration-mock' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\hardware\scale-calibration-mock\build.gradle'.
Evaluating project ':hardware:shared' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\hardware\shared\build.gradle'.
Evaluating project ':jee:war' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\jee\war\build.gradle'.
Compiling build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\jee\war\build.gradle' using BuildScriptClasspathScriptTransformer.
Compiling build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\jee\war\build.gradle' using BuildScriptTransformer.
:: loading settings :: url = jar:file:/C:/java/gradle-1.0-milestone-2/lib/ivy-2.2.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
:: resolving dependencies :: com.dp.connect.jee#war;1.0.0-SNAPSHOT
confs: [webstart]
found com.dp.connect.bootstrap#client;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.bootstrap#client;1.0.0-SNAPSHOT (forced)
found org.codehaus.groovy#groovy;1.8.0 in MavenRepo
found antlr#antlr;2.7.7 in MavenRepo
found asm#asm;3.2 in MavenRepo
found asm#asm-commons;3.2 in MavenRepo
found asm#asm-tree;3.2 in MavenRepo
found asm#asm-util;3.2 in MavenRepo
found asm#asm-analysis;3.2 in MavenRepo
found com.dp.connect.framework#client;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.framework#client;1.0.0-SNAPSHOT (forced)
found com.dp.connect.framework#facade;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.framework#facade;1.0.0-SNAPSHOT (forced)
found com.dp.connect.framework#shared;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.framework#shared;1.0.0-SNAPSHOT (forced)
found commons-math#commons-math;1.2 in MavenRepo
found commons-lang#commons-lang;2.4 in MavenRepo
found commons-beanutils#commons-beanutils;1.8.3 in MavenRepo
found commons-logging#commons-logging;1.1.1 in MavenRepo
found commons-collections#commons-collections;3.2.1 in MavenRepo
found log4j#log4j;1.2.16 in MavenRepo
found com.dp.connect.label-printing#shared;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.label-printing#shared;1.0.0-SNAPSHOT (forced)
found org.springframework#spring-beans;3.0.5.RELEASE in MavenRepo
found org.springframework#spring-core;3.0.5.RELEASE in MavenRepo
found org.springframework#spring-asm;3.0.5.RELEASE in MavenRepo
found org.springframework#spring-aop;3.0.5.RELEASE in MavenRepo
found aopalliance#aopalliance;1.0 in MavenRepo
found org.springframework#spring-context;3.0.5.RELEASE in MavenRepo
found org.springframework#spring-expression;3.0.5.RELEASE in MavenRepo
found org.springframework#spring-web;3.0.5.RELEASE in MavenRepo
found com.jgoodies#forms;1.1.0 in MavenRepo
found com.jgoodies#binding;2.0.1-extensible in http://atlno-stage01.newops.dhlgm.corp/mvn_repository_contribution/
found com.jgoodies#validation;2.0.0 in MavenRepo
found org.jdesktop#swingworker;1.1 in http://atlno-stage01.newops.dhlgm.corp/mvn_repository_contribution/
found org.jdesktop#swingx;2007_09_16 in http://atlno-stage01.newops.dhlgm.corp/mvn_repository_contribution/
found commons-cli#commons-cli;1.2 in MavenRepo
found jasperreports#jasperreports;3.0.0 in MavenRepo
found commons-collections#commons-collections;3.2.1 in MavenRepo
[3.2.1] commons-collections#commons-collections;[2.1,)
found commons-digester#commons-digester;2.1 in MavenRepo
[2.1] commons-digester#commons-digester;[1.7,)
found commons-logging#commons-logging;1.1.1 in MavenRepo
[1.1.1] commons-logging#commons-logging;[1.0,)
found jfree#jcommon;1.0.2 in MavenRepo
[1.0.2] jfree#jcommon;[1.0.0,)
found xml-apis#xml-apis;1.3.02 in MavenRepo
found eclipse#jdtcore;3.2.0.v_658 in MavenRepo
[3.2.0.v_658] eclipse#jdtcore;[3.1.0,)
found com.lowagie#itext;2.0.1 in MavenRepo
found jfree#jfreechart;1.0.2 in MavenRepo
found commons-httpclient#commons-httpclient;3.1 in MavenRepo
found commons-codec#commons-codec;1.2 in MavenRepo
found com.dp.connect.encoding#client;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.encoding#client;1.0.0-SNAPSHOT (forced)
found com.dp.connect.encoding#facade;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.encoding#facade;1.0.0-SNAPSHOT (forced)
found com.dp.connect.encoding#shared;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.encoding#shared;1.0.0-SNAPSHOT (forced)
found com.dp.connect.label-printing#client;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.label-printing#client;1.0.0-SNAPSHOT (forced)
found com.dp.connect.hardware#label-printer;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.hardware#label-printer;1.0.0-SNAPSHOT (forced)
found com.dp.connect.hardware#shared;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.hardware#shared;1.0.0-SNAPSHOT (forced)
found com.dp.connect.hardware#scale-calibration;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.hardware#scale-calibration;1.0.0-SNAPSHOT (forced)
found com.dp.connect.hardware#scale;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.hardware#scale;1.0.0-SNAPSHOT (forced)
found javax.comm.custom#commw32;1.0 in clientModuleChain
found javax.comm.custom#commws;1.0 in clientModuleChain
found javax.comm.custom#win32com;1.0 in clientModuleChain
found com.dp.connect.hardware#scale-calibration-mock;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.hardware#scale-calibration-mock;1.0.0-SNAPSHOT (forced)
found com.dp.connect.hardware#barcode-scanner;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.hardware#barcode-scanner;1.0.0-SNAPSHOT (forced)
found com.dp.connect.routing-matrix#server;1.0.0-SNAPSHOT in internal-repository
[1.0.0-SNAPSHOT] com.dp.connect.routing-matrix#server;1.0.0-SNAPSHOT (forced)
:: resolution report :: resolve 4844ms :: artifacts dl 0ms
:: evicted modules:
commons-beanutils#commons-beanutils;1.7.0 by commons-beanutils#commons-beanutils;1.8.3 in [webstart]
jfree#jcommon;1.0.0 by jfree#jcommon;1.0.2 in [webstart]
commons-logging#commons-logging;1.0.4 by commons-logging#commons-logging;1.1.1 in [webstart]
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Evaluating project ':label-printing:client' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\label-printing\client\build.gradle'.
Evaluating project ':label-printing:facade' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\label-printing\facade\build.gradle'.
Evaluating project ':label-printing:server' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\label-printing\server\build.gradle'.
Evaluating project ':label-printing:shared' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\label-printing\shared\build.gradle'.
Evaluating project ':routing-matrix:api' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\routing-matrix\api\build.gradle'.
Evaluating project ':routing-matrix:server' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\routing-matrix\server\build.gradle'.
Evaluating project ':routing-matrix:test-bench' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\routing-matrix\test-bench\build.gradle'.
Evaluating project ':sort-programs:api' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\sort-programs\api\build.gradle'.
Evaluating project ':sort-programs:server' using build file 'C:\work\trunk\Core\r2\Development\Sources\xbo\sort-programs\server\build.gradle'.
All projects evaluated.