@defaultMessage spawns threads with vague names; use a custom thread factory and name threads so that you can tell (by its name) which executor it is associated with

java.util.concurrent.Executors#newFixedThreadPool(int)
java.util.concurrent.Executors#newSingleThreadExecutor()
java.util.concurrent.Executors#newCachedThreadPool()
java.util.concurrent.Executors#newSingleThreadScheduledExecutor()
java.util.concurrent.Executors#newScheduledThreadPool(int)
java.util.concurrent.Executors#defaultThreadFactory()
java.util.concurrent.Executors#privilegedThreadFactory()

java.lang.Character#codePointBefore(char[],int) @ Implicit start offset is error-prone when the char[] is a buffer and the first chars are random chars
java.lang.Character#codePointAt(char[],int) @ Implicit end offset is error-prone when the char[] is a buffer and the last chars are random chars

@defaultMessage Collections.sort dumps data into an array, sorts the array and reinserts data into the list, one should rather use Lucene's CollectionUtil sort methods which sort in place

java.util.Collections#sort(java.util.List)
java.util.Collections#sort(java.util.List,java.util.Comparator)

java.io.StringReader#<init>(java.lang.String) @ Use FastStringReader instead

org.apache.lucene.util.RamUsageEstimator#sizeOf(java.lang.Object) @ This can be a perfromance trap 

@defaultMessage Reference management is tricky, leave it to SearcherManager
org.apache.lucene.index.IndexReader#decRef()
org.apache.lucene.index.IndexReader#incRef()
org.apache.lucene.index.IndexReader#tryIncRef()

org.apache.lucene.index.IndexWriter#maybeMerge() @ use Merges#maybeMerge
org.apache.lucene.index.IndexWriter#forceMerge(int) @ use Merges#forceMerge
org.apache.lucene.index.IndexWriter#forceMerge(int,boolean) @ use Merges#forceMerge
org.apache.lucene.index.IndexWriter#forceMergeDeletes() @ use Merges#forceMergeDeletes
org.apache.lucene.index.IndexWriter#forceMergeDeletes(boolean) @ use Merges#forceMergeDeletes

@defaultMessage QueryWrapperFilter is cachable by default - use Queries#wrap instead
org.apache.lucene.search.QueryWrapperFilter#<init>(org.apache.lucene.search.Query)

@defaultMessage Only use wait / notify when really needed try to use concurrency primitives, latches or callbacks instead. 
java.lang.Object#wait()
java.lang.Object#wait(long)
java.lang.Object#wait(long,int)
java.lang.Object#notify()
java.lang.Object#notifyAll()

@defaultMessage Beware of the behavior of this method on MIN_VALUE
java.lang.Math#abs(int)
java.lang.Math#abs(long)

@defaultMessage Use Long.compare instead we are on Java7
com.google.common.primitives.Longs#compare(long,long)