Revision history for Deobfuscator

0.0.1  Fri Apr  7 14:34:50 2006
       Initial release.

0.0.2  Mon Apr 24 13:27:52 CDT 2006
       NEW: Laura's cool flowchart added, which shows how the Deobfuscator
            works. Updated README and deob_help.html to reflect that.
       FIX: Cryptic "Can't close MODS file" error message rewritten.
       NEW: Indulged my POD formatting obsession. Again. (Lots of minor
            updates to the POD)
       NEW: Added Feedback section to deob_help.html.
       NEW: Added DOCUMENTATION section to README.
       FIX: "About the mailing lists" URL changed throughout.

0.0.3  Mon Oct  2 20:01:45 CDT 2006
       FIX: change default $deob_detail_path to be a relative URL instead of
            having localhost hardcoded. Thanks to Jason Stajich for pointing
            this out.
       FIX: Bio::Ontology modules are no longer missing their prefix in the
            class list, and their methods are now shown in the lower pane
            as expected. Thanks to Hilmar Lapp for reporting this bug.
       FIX: can now handle (and ignore) VERSION POD section.
       FIX: missing SYNOPSIS section now handled properly. In fact, the
            SYNOPSIS and DESCRIPTION sections can be in reverse order now,
            although for consistency this is not recommended.
       FIX: Bug #2114: "Obfuscator doesn't show "Bio:Matrix:Generic" has been
            fixed. This bug turned out to afflict multiple modules, which
            weren't getting parsed correctly by deob_index.pl.
       NEW: Table cells have been padded out to get rid of that "scrunched"
            look. Thanks to Sendu Bala for this great suggestion.
       NEW: If the 'Returns' subsection of a method's documentation contains
            a POD L<> link, the Deobfuscator assumes this to be a package
            name, and wraps it in an href for display. This feature is
            not robust, but seems to work well enough for now.
       NEW: the list of classes is now sorted alphabetically depth-first, so
            that subclasses appear just after their parent class. Thanks to
            Amir Karger for noticing the strange sorting behavior.
       NEW: HTML page title now 'BioPerl Deobfuscator' to distinguish it from
            other Deobfuscators out there. Thanks to Amir Karger for
            suggesting this.
       NEW: 'No match' search string now more prominent. Yep, kudos to Amir
            Karger again -- another great idea!
       NEW: Search box caption now explicitly states that only package names
            can be searched. Big ups to Amir Karger for this suggestion.
            The ability to search method names is planned for a future version.
       NEW: added -x option to deob_index.pl. This allows the use of an
            'excluded modules' file. This feature was added to resolve an
            issue with four modules which rely on external modules to compile.
            Class::Inspector, used by the Deobfuscator needs to load a
            module to traverse its inheritance tree, and modules must compile
            before they can be loaded.
    CHANGE: using short name now when traversing with File::Find to help
            identify excluded modules (deob_index.pl).

Added since 0.0.3:
        NEW: deob_index.pl can now accept relative paths for BioPerl lib dir
             and output dir
        NEW: -s <version_string> option now can be passed to deob_index.pl to
             store a version string in packages.db which deob_interface.cgi
             can read and show.