Bugs fixed:
 * A serious error in copymat which caused incorrect databases to be
   produced has been fixed.
 * A number of problems with query concatenation in blastall have been fixed.
 * XML output was brought in sync with text output by adding masking of the 
   filtered locations in query sequences.

Changes:
 * formatdb can no longer produce old-style BLAST databases.

Performance improvements:
 * For translating searches of large sequences, only the needed pieces of
   the sequence are translated during the traceback.
 * The performance of reading binary gilists has been improved.
 * formatdb now produces 1 gigabyte volumes by default on 32-bit platforms
   in order to prevent mmap() failures.
 * When possible, use approximate sequence lengths for search space calculation.
 * DUST filtering was made more aggressive.

Statistical improvements:
 * Unified handling of gapped Karlin blocks between protein and nucleotide
   cases.
 * Adjustments to the lengths of query and database sequences have been
   improved.
 * Composition-based statistics routines were refactored.

Ongoing software engineering improvements:
 * Fixed memory leaks.
 * Fixed uninitialized variables.
 * Fixed null pointer handling.
 * Dead code and variables were eliminated.
 * Many compiler/type warnings fixed.