Update: I tried building the org.eclipse.ptp.rm.lml-feature using my new plugins (which are under this feature or none at all). This failed to install with a similar but different set of errors:
Cannot complete the install because of a conflicting dependency.
Software being installed: PTP LML Support 5.0.5.201201261437 (org.eclipse.ptp.rm.lml.feature.group 5.0.5.201201261437)
Software currently installed: Eclipse IDE for Parallel Application Developers 1.4.1.20110911-0506 (epp.package.parallel 1.4.1.20110911-0506)
Software currently installed: PTP Common Utilities 5.0.4.201111121445 (org.eclipse.ptp.utils.feature.group 5.0.4.201111121445)
Only one of the following can be installed at once:
PTP LML Support 5.0.5.201201261437 (org.eclipse.ptp.rm.lml.feature.jar 5.0.5.201201261437)
PTP LML Support 5.0.2.201109141657 (org.eclipse.ptp.rm.lml.feature.jar 5.0.2.201109141657)
PTP LML Support 5.0.1.201107131351 (org.eclipse.ptp.rm.lml.feature.jar 5.0.1.201107131351)
PTP LML Support 5.0.4.201111121445 (org.eclipse.ptp.rm.lml.feature.jar 5.0.4.201111121445)
PTP LML Support 5.0.0.201106140904 (org.eclipse.ptp.rm.lml.feature.jar 5.0.0.201106140904)
PTP LML Support 5.0.3.201110141146 (org.eclipse.ptp.rm.lml.feature.jar 5.0.3.201110141146)
Only one of the following can be installed at once:
PTP Common Utilities 5.0.2.201109141657 (org.eclipse.ptp.utils.feature.jar 5.0.2.201109141657)
PTP Common Utilities 5.0.1.201107131351 (org.eclipse.ptp.utils.feature.jar 5.0.1.201107131351)
PTP Common Utilities 5.0.4.201111121445 (org.eclipse.ptp.utils.feature.jar 5.0.4.201111121445)
PTP Common Utilities 5.0.0.201106140904 (org.eclipse.ptp.utils.feature.jar 5.0.0.201106140904)
PTP Common Utilities 5.0.3.201110141146 (org.eclipse.ptp.utils.feature.jar 5.0.3.201110141146)
Cannot satisfy dependency:
From: Eclipse IDE for Parallel Application Developers 1.4.1.20110911-0506 (epp.package.parallel 1.4.1.20110911-0506)
To: org.eclipse.epp.package.parallel.feature.feature.group [1.4.1.20110911-0506]
Cannot satisfy dependency:
From: EPP Parallel Feature 1.4.1.20110911-0506 (org.eclipse.epp.package.parallel.feature.feature.group 1.4.1.20110911-0506)
To: org.eclipse.ptp.feature.group 0.0.0
Cannot satisfy dependency:
From: Parallel Tools Platform (PTP) End-User Runtime 5.0.0.201106140904 (org.eclipse.ptp.feature.group 5.0.0.201106140904)
To: org.eclipse.ptp.utils.feature.group [5.0.0.201106140904]
Cannot satisfy dependency:
From: Parallel Tools Platform (PTP) End-User Runtime 5.0.1.201107131351 (org.eclipse.ptp.feature.group 5.0.1.201107131351)
To: org.eclipse.ptp.utils.feature.group [5.0.1.201107131351]
Cannot satisfy dependency:
From: Parallel Tools Platform (PTP) End-User Runtime 5.0.2.201109141657 (org.eclipse.ptp.feature.group 5.0.2.201109141657)
To: org.eclipse.ptp.utils.feature.group [5.0.2.201109141657]
Cannot satisfy dependency:
From: Parallel Tools Platform (PTP) End-User Runtime 5.0.3.201110141146 (org.eclipse.ptp.feature.group 5.0.3.201110141146)
To: org.eclipse.ptp.utils.feature.group [5.0.3.201110141146]
Cannot satisfy dependency:
From: Parallel Tools Platform (PTP) End-User Runtime 5.0.4.201111121445 (org.eclipse.ptp.feature.group 5.0.4.201111121445)
To: org.eclipse.ptp.rm.lml.feature.group [5.0.4.201111121445]
Cannot satisfy dependency:
From: PTP LML Support 5.0.4.201111121445 (org.eclipse.ptp.rm.lml.feature.group 5.0.4.201111121445)
To: org.eclipse.ptp.rm.lml.feature.jar [5.0.4.201111121445]
Cannot satisfy dependency:
From: PTP LML Support 5.0.5.201201261437 (org.eclipse.ptp.rm.lml.feature.group 5.0.5.201201261437)
To: org.eclipse.ptp.rm.lml.feature.jar [5.0.5.201201261437]
Cannot satisfy dependency:
From: PTP Common Utilities 5.0.0.201106140904 (org.eclipse.ptp.utils.feature.group 5.0.0.201106140904)
To: org.eclipse.ptp.utils.feature.jar [5.0.0.201106140904]
Cannot satisfy dependency:
From: PTP Common Utilities 5.0.1.201107131351 (org.eclipse.ptp.utils.feature.group 5.0.1.201107131351)
To: org.eclipse.ptp.utils.feature.jar [5.0.1.201107131351]
Cannot satisfy dependency:
From: PTP Common Utilities 5.0.2.201109141657 (org.eclipse.ptp.utils.feature.group 5.0.2.201109141657)
To: org.eclipse.ptp.utils.feature.jar [5.0.2.201109141657]
Cannot satisfy dependency:
From: PTP Common Utilities 5.0.3.201110141146 (org.eclipse.ptp.utils.feature.group 5.0.3.201110141146)
To: org.eclipse.ptp.utils.feature.jar [5.0.3.201110141146]
Cannot satisfy dependency:
From: PTP Common Utilities 5.0.4.201111121445 (org.eclipse.ptp.utils.feature.group 5.0.4.201111121445)
To: org.eclipse.ptp.utils.feature.jar [5.0.4.201111121445]