JIRA indexing breaks on unattached custom fields in old data

A user has reported the following error when importing JIRA 2.0.2 data. The reindex after the upgrade fails with a NullPointerException:

2003-11-17 15:51:41,113 WARN [jira.issue.index.DefaultIndexManager] There was an exception whilst reindexing issue XYZjava.lang.NullPointerException
java.lang.NullPointerException
at com.atlassian.jira.issue.comparator.CustomFieldComparator.compareProjects(CustomFieldComparator.java:100)
at com.atlassian.jira.issue.comparator.CustomFieldComparator.compare(CustomFieldComparator.java:41)
at java.util.Arrays.mergeSort(Arrays.java:1241)
at java.util.Arrays.mergeSort(Arrays.java:1248)
at java.util.Arrays.mergeSort(Arrays.java:1248)
at java.util.Arrays.sort(Arrays.java:1188)
at java.util.Collections.sort(Collections.java:153)
at com.atlassian.jira.issue.managers.DefaultCustomFieldManager.getCustomFieldsFromDB(DefaultCustomFieldManager.j
ava:238)
at com.atlassian.jira.issue.managers.DefaultCustomFieldManager.populateCache(DefaultCustomFieldManager.java:360)

at com.atlassian.jira.issue.managers.DefaultCustomFieldManager.getCustomField(DefaultCustomFieldManager.java:84)

at com.atlassian.jira.issue.index.IssueDocument.getDocument(IssueDocument.java:79)
at com.atlassian.jira.issue.index.DefaultIndexManager.indexIssueAndComments(DefaultIndexManager.java:186)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexIssues(DefaultIndexManager.java:113)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:76)
at com.atlassian.jira.upgrade.tasks.AbstractReindexUpgradeTask.doUpgrade(AbstractReindexUpgradeTask.java:17)
at com.atlassian.jira.upgrade.UpgradeManagerImpl.doUpgradeTaskSucess(UpgradeManagerImpl.java:565)
at com.atlassian.jira.upgrade.UpgradeManagerImpl.doUpgrade(UpgradeManagerImpl.java:318)
at com.atlassian.jira.upgrade.UpgradeManagerImpl.doUpgradeIfNeeded(UpgradeManagerImpl.java:264)
at com.atlassian.jira.upgrade.UpgradeManagerImpl.doUpgradeIfNeededAndAllowed(UpgradeManagerImpl.java:252)
at com.atlassian.jira.upgrade.UpgradeLauncher.contextInitialized(UpgradeLauncher.java:70)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3271)

It looks like back in 2.0.2, JIRA did not delete a project's custom fields when deleting the project. As a result there are custom fields floating around without an associated project, and this kills indexing.