One of the things that changed from Solr 1.4.1 to 1.5+ was the introduction of a parameter to tell Solr / Lucene which kind of compability version its index files should be created and used in.
Solr now refuses to start if you do not provide this setting (if you’re upgrading a previous installation from 1.4.1 or earlier). The fix isn’t really straight forward, and you’ll probably have to recreate your index files if you’re just arriving at the scene with Solr / Lucene 3.2 and 4.0. Solr 3.0 (1.5) might be able to upgrade the files from the 2.9 version, but if you’re jumping from Lucene 2.9 to 4.0, the easiest solution seems to be to delete the current index and reindex (set up replication, disable replication from the master, query the slave while reindexing the master, etc.. and you’ll have no downtime while doing this!).
You’ll need to add a parameter to your solrconfig.xml file as well in the <config> section.
Other valid values are LUCENE_30, LUCENE_31, LUCENE_32 and LUCENE_40. These values represent specific versions of the index structure, while LUCENE_CURRENT will use the version depending on which particular release of Lucene you’re using. The version format will be upgraded automagically between most releases, so you’ll probably be fine by using LUCENE_CURRENT. If you however are trying to load index files that are more than one version older, you may have to use one of the other values.