bisect: clean flags after checking merge bases

Unless there is a good reason to belieave that a particular
invocation of a get_merge_bases*() is the last one that cares about
the object flags the computation of merge bases leaves on the
objects, the "cleanup" parameter should always be true, and I do not
think there is one in this codepath.

Found by code inspection.

Signed-off-by: Junio C Hamano <gitster@pobox.com>
get_merge_bases(): always clean-up object flags

The callers of get_merge_bases() can choose to leave object flags
used during the merge-base traversal by passing cleanup=0 as a
parameter, but in practice a very few callers can afford to do so
(namely, "git merge-base"), as they need to compute merge base in
preparation for other processing of their own and they need to see
the object without contaminate flags.

Change the function signature of get_merge_bases_many() and
get_merge_bases() to drop the cleanup parameter, so that the
majority of the callers do not have to say ", 1" at the end.

Give a new get_merge_bases_many_dirty() API to support only a few
callers that know they do not need to spend cycles cleaning up the
object flags.

Signed-off-by: Junio C Hamano <gitster@pobox.com>
lockfile.c: store absolute path

Locked paths can be saved in a linked list so that if something wrong
happens, *.lock are removed. For relative paths, this works fine if we
keep cwd the same, which is true 99% of time except:

- update-index and read-tree hold the lock on $GIT_DIR/index really
  early, then later on may call setup_work_tree() to move cwd.

- Suppose a lock is being held (e.g. by "git add") then somewhere
  down the line, somebody calls real_path (e.g. "link_alt_odb_entry"),
  which temporarily moves cwd away and back.

During that time when cwd is moved (either permanently or temporarily)
and we decide to die(), attempts to remove relative *.lock will fail,
and the next operation will complain that some files are still locked.

Avoid this case by turning relative paths to absolute before storing
the path in "filename" field.

Reported-by: Yue Lin Ho <yuelinho777@gmail.com>
Helped-by: Ramsay Jones <ramsay@ramsay1.demon.co.uk>
Helped-by: Johannes Sixt <j6t@kdbg.org>
Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Adapted-by: Michael Haggerty <mhagger@alum.mit.edu>
Signed-off-by: Michael Haggerty <mhagger@alum.mit.edu>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
docs/credential-store: s/--store/--file/

The option name "--store" was used early in development, but
never even made it into an applied patch, let alone a
released version of git. I forgot to update the matching
documentation at the time, though.

Noticed-by: Jesse Hopkins <jesse.hopkins@lmco.com>
Signed-off-by: Jeff King <peff@peff.net>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
Merge branch 'jk/cache-tree-protect-from-broken-libgit2'

The code to use cache-tree trusted the on-disk data too much
and fell into an infinite loop.

* jk/cache-tree-protect-from-broken-libgit2:
  cache-tree: avoid infinite loop on zero-entry tree
Merge branch 'rs/use-child-process-init-more'

* rs/use-child-process-init-more:
  bundle: split out ref writing from bundle_create
  bundle: split out a helper function to compute and write prerequisites
  bundle: split out a helper function to create pack data
  use child_process_init() to initialize struct child_process variables
Merge branch 'jk/fetch-reflog-df-conflict'

Corner-case bugfixes for "git fetch" around reflog handling.

* jk/fetch-reflog-df-conflict:
  ignore stale directories when checking reflog existence
  fetch: load all default config at startup
Merge branch 'tm/line-log-first-parent'

"git log --first-parent -L..." used to crash.

* tm/line-log-first-parent:
  line-log: fix crash when --first-parent is used
Merge branch 'nd/gitignore-trailing-whitespace'

Documentation update.

* nd/gitignore-trailing-whitespace:
  gitignore.txt: fix spelling of "backslash"
Merge branch 'maint'

* maint:
  docs/credential-store: s/--store/--file/
Merge branch 'nd/lockfile-absolute' into next

The lockfile API can get confused which file to clean up when the
process moved the $cwd after creating a lockfile.

* nd/lockfile-absolute:
  lockfile.c: store absolute path
Merge branch 'jc/merge-bases' into next

* jc/merge-bases:
  get_merge_bases(): always clean-up object flags
  bisect: clean flags after checking merge bases
Merge branch 'master' into next

* master:
  docs/credential-store: s/--store/--file/
Git 2.2.0-rc1

Signed-off-by: Junio C Hamano <gitster@pobox.com>
Sync with 2.2-rc1

* master:
  Git 2.2.0-rc1