This patch was created by running the following commands:

for i in */*[ch]; do doxygenify.pl $i; done
perl -i -pe 's#\*{3} \*/$#****/#' */*[ch]

where doxygenify.pl is
https://svn.innodb.com/svn/misc/trunk/tools/doxygenify.pl r510

Verified the consistency as follows:

(0) not too many /* in: */ or /* out: */ comments left in the code:
grep -l '/\*\s*\(in\|out\)[,:/]' */*[ch]

(1) no difference when ignoring blank lines, after stripping all
C90-style /* comments */, including multi-line ones, before and after
applying this patch:

perl -i -e 'undef $/;while(<ARGV>){s#/\*(.*?)\*/##gs;print}' */*[ch]
diff -I'^\s*$' --exclude .svn -ru TREE1 TREE2

(2) after stripping @return comments and !<, generated a diff and omitted
the hunks where /* out: */ function return comments were removed:

perl -i -e'undef $/;while(<ARGV>){s#!<##g;s#\n\@return\t.*?\*/# \*/#gs;print}'\
 */*[ch]
svn diff|
perl -e 'undef $/;$_=<>;s#\n-\s*/\* out[:,]([^\n]*?)(\n-[^\n]*?)*\*/##gs;print'

Some unintended changes were left.  These will be removed in a
subsequent patch.

Whitespace fixup.

Document the function parameters.

now that the function was declared void in r5060.

srv0start.c does not (any longer) call memcmp.
srv_parse_megabytes(): Add a function comment.

and add a const qualifier that was missing.

transactions that are started before the rollback of incomplete
transactions has finished may have an inconsistent view of the
secondary indexes.

dict_index_is_sec_or_ibuf(): Auxiliary function for controlling
updates and checks of PAGE_MAX_TRX_ID: check whether an index is a
secondary index or the insert buffer tree.

page_set_max_trx_id(), page_update_max_trx_id(),
lock_rec_insert_check_and_lock(),
lock_sec_rec_modify_check_and_lock(), btr_cur_ins_lock_and_undo(),
btr_cur_upd_lock_and_undo(): Add the parameter mtr.

page_set_max_trx_id(): Allow mtr to be NULL.  When mtr==NULL, do not
attempt to write to the redo log.  This only occurs when creating a
page or reorganizing a compressed page.  In these cases, the
PAGE_MAX_TRX_ID will be set correctly during the application of redo
log records, even though there is no explicit log record about it.

btr_discard_only_page_on_level(): Preserve PAGE_MAX_TRX_ID.  This
function should be unreachable, though.

btr_cur_pessimistic_update(): Update PAGE_MAX_TRX_ID.

Add some assertions for checking that PAGE_MAX_TRX_ID is set on all
secondary index leaf pages.

rb://115 tested by Michael, fixes Issue #211

function declarations from <atomic.h>.
Call the functions with proper arguments.

Add missing out: comments.

correctly estimate the free space on the compressed page by
page_zip_available(..., create=TRUE). This was reported as Issue #231.

btr_cur_update_alloc_zip(): Add the parameter ibool create and pass it
to page_zip_available(). The parameter was previously passed as 0.

btr_cur_optimistic_update(): Pass create=TRUE to btr_cur_update_alloc_zip().

rb://120 approved by Heikki Tuuri

Add ChangeLog entry for r4994.

  ------------------------------------------------------------------------
  r4994 | marko | 2009-05-14 15:04:55 +0300 (Thu, 14 May 2009) | 18 lines

  branches/5.1: Prevent a race condition in innobase_commit() by ensuring
  that innodb_commit_concurrency>0 remains constant at run time. (Bug #42101)

  srv_commit_concurrency: Make this a static variable in ha_innodb.cc.

  innobase_commit_concurrency_validate(): Check that innodb_commit_concurrency
  is not changed from or to 0 at run time.  This is needed, because
  innobase_commit() assumes that innodb_commit_concurrency>0 remains constant.
  Without this limitation, the checks for innodb_commit_concurrency>0
  in innobase_commit() should be removed and that function would have to
  acquire and release commit_cond_m at least twice per invocation.
  Normally, innodb_commit_concurrency=0, and introducing the mutex operations
  would mean significant overhead.

  innodb_bug42101.test, innodb_bug42101-nonzero.test: Test cases.

  rb://123 approved by Heikki Tuuri
  ------------------------------------------------------------------------

Add ChangeLog entry for r4977.

  ------------------------------------------------------------------------
  r4976 | marko | 2009-05-13 15:44:54 +0300 (Wed, 13 May 2009) | 6 lines

  branches/5.1: Display DB_ROLL_PTR in the COLUMNS section of the
  innodb_table_monitor output.  It was accidentally omitted due to an
  off-by-one loop condition.  (Bug #44320)

  rb://116 approved by Heikki Tuuri
  ------------------------------------------------------------------------

This addresses Mantis Issue #23 in InnoDB Hot Backup and some
of MySQL Bug #41609.

In MLOG_FILE_CREATE, we need to distinguish temporary tables, so that
InnoDB Hot Backup can work correctly.  It turns out that we can do this
easily, by using a bit of the previously unused parameter for page number.
(The page number parameter of MLOG_FILE_CREATE has been written as 0 
ever since MySQL 4.1, which introduced MLOG_FILE_CREATE.)

MLOG_FILE_FLAG_TEMP: A flag for indicating a temporary table in
the page number parameter of MLOG_FILE_ operations.

fil_op_write_log(): Add the parameter log_flags.

fil_op_log_parse_or_replay(): Add the parameter log_flags.
Do not replay MLOG_FILE_CREATE when MLOG_FILE_FLAG_TEMP is set in log_flags.
This only affects ibbackup --apply-log.  InnoDB itself never replays file
operations.

rb://117 approved by Heikki Tuuri

The insert buffer tree is a clustered index.

prebuilt->index_usable, as suggested by Michael.