@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()

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

@defaultMessage Because the filtercache doesn't take deletes into account FilteredQuery can't be used - use XFilteredQuery instead
org.apache.lucene.search.FilteredQuery#<init>(org.apache.lucene.search.Query,org.apache.lucene.search.Filter)
org.apache.lucene.search.FilteredQuery#<init>(org.apache.lucene.search.Query,org.apache.lucene.search.Filter,org.apache.lucene.search.FilteredQuery$FilterStrategy)

@defaultMessage Pass the precision step from the mappings explicitly instead
org.apache.lucene.search.NumericRangeQuery#newDoubleRange(java.lang.String,java.lang.Double,java.lang.Double,boolean,boolean)
org.apache.lucene.search.NumericRangeQuery#newFloatRange(java.lang.String,java.lang.Float,java.lang.Float,boolean,boolean)
org.apache.lucene.search.NumericRangeQuery#newIntRange(java.lang.String,java.lang.Integer,java.lang.Integer,boolean,boolean)
org.apache.lucene.search.NumericRangeQuery#newLongRange(java.lang.String,java.lang.Long,java.lang.Long,boolean,boolean)
org.apache.lucene.search.NumericRangeFilter#newDoubleRange(java.lang.String,java.lang.Double,java.lang.Double,boolean,boolean)
org.apache.lucene.search.NumericRangeFilter#newFloatRange(java.lang.String,java.lang.Float,java.lang.Float,boolean,boolean)
org.apache.lucene.search.NumericRangeFilter#newIntRange(java.lang.String,java.lang.Integer,java.lang.Integer,boolean,boolean)
org.apache.lucene.search.NumericRangeFilter#newLongRange(java.lang.String,java.lang.Long,java.lang.Long,boolean,boolean)

@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)

@defaultMessage we have an optimized XStringField to reduce analysis creation overhead
org.apache.lucene.document.Field#<init>(java.lang.String,java.lang.String,org.apache.lucene.document.FieldType)