Merge branch 'master' of ssh://git-annex.branchable.com

doc/bugs/git-annex-fsck_fails___34__thread_blocked_indefinitely_in_an_STM_transaction__34__.mdwn

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+### Please describe the problem.
+
+Running git-annex-fsck fails with the error "thread blocked indefinitely in an STM transaction"
+
+### What steps will reproduce the problem?
+
+
+### What version of git-annex are you using? On what operating system?
+git-annex version: 7.20190708-gbc74eb1
+Amazon Linux 2 ( Linux ip-172-31-87-151.ec2.internal 4.14.133-113.105.amzn2.x86_64 #1 SMP Wed Jul 10 16:57:02 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux )
+
+### Please provide any additional information below.
+
+[[!format sh """
+# If you can, paste a complete transcript of the problem occurring here.
+# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
+git annex fsck --fast -J66 --json --json-error-messages 
+
+...
+git-annex: thread blocked indefinitely in an STM transaction
+
+
+
+(master_env_v149_py36) 11:56  [viral-ngs-benchmarks] $ git annex version
+git-annex version: 7.20190708-gbc74eb1
+build flags: Assistant Webapp Pairing S3 WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
+dependency versions: aws-0.21.1 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.3 feed-1.0.1.0 ghc-8.4.2 http-client-0.5.14 persistent-sql\
+ite-2.9.2 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.0
+key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_2\
+24 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE\
+2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256\
+ BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL
+remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar hook external
+operating system: linux x86_64
+supported repository versions: 5 7
+upgrade supported from repository versions: 0 1 2 3 4 5 6
+local repository version: 5
+(master_env_v149_py36) 12:00  [viral-ngs-benchmarks] $ uname -a
+Linux ip-172-31-87-151.ec2.internal 4.14.133-113.105.amzn2.x86_64 #1 SMP Wed Jul 10 16:57:02 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
+(
+
+# End of transcript or log.
+"""]]
+
+### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)
+
+

doc/install/Windows/comment_6_90ef5d5a4f66ac3e440aadf302a625a9._comment

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+[[!comment format=mdwn
+ username="Ilya_Shlyakhter"
+ avatar="http://cdn.libravatar.org/avatar/1647044369aa7747829c38b9dcc84df0"
+ subject="error when building on windows"
+ date="2019-07-22T18:04:29Z"
+ content="""
+Building on Windows gives this error:
+
+[[!format sh \"\"\"
+Extracting  ghc-8.6.5.tar
+
+Everything is Ok
+
+Size:       1773445120
+Compressed: 280280296
+Extracting ghc-8.6.5.tar...
+Extracted total of 9780 files from ghc-8.6.5.tar
+C:\Users\ilya\AppData\Local\Programs\stack\x86_64-windows\ghc-8.6.5-tmp6568\ghc-8.6.5\: renamePath:MoveFileEx \"C:\\Users\\ilya\\AppData\\Local\\Programs\\stack\\x86_64-windows\\ghc-8.6.5-tmp6568\\ghc-8.6.5\\\" \"C:\\Users\\ilya\\AppData\\Local\\Programs\\stack\\x86_64-windows\\ghc-8.6.5\\\": permission denied (Access is denied.)
+
+\"\"\"]]
+
+Running Git Bash with Administrator privileges does not seem to help.  Anyone else run into this / know how to fix it?  Thanks!
+"""]]

doc/todo/sync_--branches__to_sync_only_specified_branches___40__e.g._git-annex__41__/comment_3_bab52f2fd4f66cac6a178cdd9ef71c6d._comment

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+[[!comment format=mdwn
+ username="Dan"
+ avatar="http://cdn.libravatar.org/avatar/45b0925215b6b772921a50eca1f55b55"
+ subject="Still Wanted"
+ date="2019-07-22T17:06:20Z"
+ content="""
+Thanks for directing me here from our conversation on the [git-sync page](http://git-annex.branchable.com/sync/).
+
+RE your [first comment here](http://git-annex.branchable.com/todo/sync_--branches__to_sync_only_specified_branches___40__e.g._git-annex__41__/#comment-f5d79cf275bac5578a05cfb9f5b66292) this sounds like the behavior I'm looking for, and in particular for `git annex sync --branch git-annex` to be a special case (ideally configurable so I don't have to type it all the time); not sure if it should be handled by `git`'s config or tracked in the `git-annex` branch, but probably the former (since otherwise the behavior could change pre and post sync, which might be surprising).
+
+I'm trying to understand your [second comment](http://git-annex.branchable.com/todo/sync_--branches__to_sync_only_specified_branches___40__e.g._git-annex__41__/#comment-96120307c5584a563e4bf3ca3c4c3df3). I'm not 100% clear on what `git annex sync` actually does under the hood; if it's pushing and pulling, then presumably I'd need to tweak the git config entries for `remote.name.{push,pull}`, no? OTOH, with the `synced/` branch workflow, perhaps it's fetching, then merging, then pushing, and that's why I should tweak the fetch settings? This would need to get set for *all* of my remotes too, right?
+
+Assuming I'm understanding correctly, the downside to this approach is that it would also change the way base `git` works. Really, I'm looking for a workflow where `git annex` is (insofar as possible) narrowly responsible for managing the annex, and base `git` is responsible for everything it normally is. This would let me minimally modify my git-habits and just run `git annex add` and `git annex sync --content` from time to time to make sure that things are propagating in a sensible way based on how I've configured wanted/preferences. In particular, I'd like `git fetch` to still behave in the way that it used to, I just don't want `git annex sync` pulling and pushing around my code.
+"""]]

doc/todo/sync_--branches__to_sync_only_specified_branches___40__e.g._git-annex__41__/comment_4_a765e998ffaecc2af681947263cd80d7._comment

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+[[!comment format=mdwn
+ username="Dan"
+ avatar="http://cdn.libravatar.org/avatar/986de9e060699ae70ff7c31342393adc"
+ subject="git annex sync commits changes, too?"
+ date="2019-07-22T17:25:39Z"
+ content="""
+I took a closer look at the [man page for `git-annex-sync`](http://git-annex.branchable.com/git-annex-sync/).
+
+My understanding is that running it without any options will
+
+1. commit any changes (presumably something like `commit -am 'some default message?'`)
+2. fetch and merge `synced/$(currentbranch)` and `git-annex` branches (presumably from *all* remotes unless o/w configured)
+3. push the branches from (2) back to the remotes
+
+I'm realizing that what I really want is a `git-annex-sync` command that will *just* sync `git-annex` content. The workflow I'd like is
+
+1. fetch and merge `git-annex` branch from all remotes (or as specified by arguments)
+2. push `git-annex` branch back to remotes from (1)
+3. If _content_ related flags in the style of arguments from `git-annex-sync` (e.g., `--content`) are passed, sync them around.
+
+So the command I think I'm looking for is something like `git annex sync --no-commit --branch git-annex`, but since it's still in todo, I assume the `--branch git-annex` behavior is not yet implemented. 
+Moreover, it seems I can configure the `--no-commit` option to be the default by setting the `annex.autocommit` option to false (and this setting is handled by the `git-annex` branch, with options for local override via local gitconfig). If `--branch` gets implemented, I'd love for there to be a similar config-level option like `annex.synccurrentbranch` with true giving the current (default) behavior wherein the current branch is fetch/merge/pushed, and `annex.synccurrentbranch` giving an alternate behavior akin to the hypothetical `git annex sync --branch git-annex`.
+
+Of course I think both features (adding `--branch` option to `git-annex-sync`; supporting `annex.synccurrentbranch` config) would be useful, but really just the latter would be enough for what I'm looking to do.
+
+Thanks for your consideration and for such an excellent tool; it's really been a gamechanger for me.
+"""]]