Bisecting points to 2d54aa5397cd as the source of this regression.

Related: bug 4533

The rbc reference is just a debug message and expected in this case.

Repro case with traceabck:
...
adding yt_unstable.kpf revisions
files: 2813/2813 chunks (100.00%)
added 15340 changesets with 33020 changes to 2813 files (+2 heads)
couldn't read revision branch cache names: [Errno 2] No such file or directory: '/tmp/yt/.hg/cache/rbc-names-v1'
preparing listkeys for "phases"
sending listkeys command
checking for updated bookmarks
adding remote bookmark @
adding remote bookmark development
adding remote bookmark experimental
updating the branch cache
Traceback (most recent call last):
  File "/home/mk/hg/mercurial/dispatch.py", line 140, in _runcatch
    return _dispatch(req)
  File "/home/mk/hg/mercurial/dispatch.py", line 860, in _dispatch
    cmdpats, cmdoptions)
  File "/home/mk/hg/mercurial/dispatch.py", line 621, in runcommand
    ret = _runcommand(ui, options, cmd, d)
  File "/home/mk/hg/mercurial/dispatch.py", line 951, in _runcommand
    return checkargs()
  File "/home/mk/hg/mercurial/dispatch.py", line 922, in checkargs
    return cmdfunc()
  File "/home/mk/hg/mercurial/dispatch.py", line 857, in <lambda>
    d = lambda: util.checksignature(func)(ui, *args, **cmdoptions)
  File "/home/mk/hg/mercurial/util.py", line 711, in check
    return func(*args, **kwargs)
  File "/home/mk/hg/mercurial/commands.py", line 1374, in clone
    branch=opts.get('branch'))
  File "/home/mk/hg/mercurial/hg.py", line 469, in clone
    bn = destrepo[uprev].branch()
  File "/home/mk/hg/mercurial/context.py", line 514, in branch
    return encoding.tolocal(self._changeset[5].get("branch"))
  File "/home/mk/hg/mercurial/util.py", line 450, in __get__
    result = self.func(obj)
  File "/home/mk/hg/mercurial/context.py", line 483, in _changeset
    return self._repo.changelog.read(self.rev())
  File "/home/mk/hg/mercurial/changelog.py", line 312, in read
    text = self.revision(node)
  File "/home/mk/hg/mercurial/revlog.py", line 1084, in revision
    bins = self._chunks(chain)
  File "/home/mk/hg/mercurial/revlog.py", line 991, in _chunks
    self._chunkraw(revs[0], revs[-1])
  File "/home/mk/hg/mercurial/revlog.py", line 966, in _chunkraw
    return self._getchunk(start, length)
  File "/home/mk/hg/mercurial/revlog.py", line 957, in _getchunk
    return self._loadchunk(offset, length)
  File "/home/mk/hg/mercurial/revlog.py", line 926, in _loadchunk
    df = self.opener(self.indexfile)
  File "/home/mk/hg/mercurial/changelog.py", line 116, in _divert
    return opener(name + ".a", mode)
  File "/home/mk/hg/mercurial/store.py", line 455, in __call__
    return self.vfs(self.encode(path), mode, *args, **kw)
  File "/home/mk/hg/mercurial/scmutil.py", line 424, in __call__
    fp = util.posixfile(f, mode)
IOError: [Errno 2] No such file or directory: '/tmp/yt/.hg/store/00changelog.i.a'
abort: No such file or directory: /tmp/yt/.hg/store/00changelog.i.a

(In reply to comment #1)
> Bisecting points to 2d54aa5397cd as the source of this regression.

For easy reference: http://selenic.com/repo/hg/rev/2d54aa5397cd
"changelog: rely on transaction for finalization"

Fix in progress.

Fixed by http://selenic.com/repo/hg/rev/a41902aac76d
Matt Mackall <mpm@selenic.com>
repoview: invalidate cached changelog if _delayed changes (issue4549)

Starting with 2d54aa5397cd, when a clone reached the checkout stage,
the cached changelog in the filtered view was still seeing the
_delayed flag, even though the changelog had already been finalized.

(please test the fix)

Tested with hg version 4e865115566e and the problem appears to be fixed.  Thanks for looking at this!