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

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Joey Hess 2024-07-01 11:29:38 -04:00
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188
doc/bugs/change_in_beh__58___addurls_creates_multiple_commits.mdwn Normal file
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### Please describe the problem.
Our DataLad test which explicitly tests that we are not breeding commits in git-annex branch while adding files/urls to point to datalad-archive special remote started to fail going from git-annex 10.20240532-gf9ce7a452cc0fd5cdd2d58739741f7264fdbc598 to 10.20240532-g28f5c47b5a0daf96e5ed9aa719ff1e2763d3cc8b
(invocation: `python -m pytest -s -v datalad/local/tests/test_add_archive_content.py::TestAddArchiveOptions::test_add_delete_after_and_drop_subdir`)
If before we had a single commit
<details>
<summary></summary>
```shell
❯ git log -p git-annex^..git-annex
commit b42433cab9f671d206fe937ee7b68b53f11a0c54 (git-annex)
Author: DataLad Tester <test@example.com>
Date: Sun Jun 30 10:48:16 2024 -0400
update
diff --git a/d77/a0b/MD5E-s4--ec4d1eb36b22d19728e9d1d23ca84d1c.txt.log b/d77/a0b/MD5E-s4--ec4d1eb36b22d19728e9d1d23ca84d1c.txt.log
new file mode 100644
index 0000000..cc638db
--- /dev/null
+++ b/d77/a0b/MD5E-s4--ec4d1eb36b22d19728e9d1d23ca84d1c.txt.log
@@ -0,0 +1,2 @@
+1719758896s 1 c04eb54b-4b4e-5755-8436-866b043170fa
+1719758897s 0 d53ab0e3-21a9-4084-806f-bf9f5812f34e
diff --git a/d77/a0b/MD5E-s4--ec4d1eb36b22d19728e9d1d23ca84d1c.txt.log.web b/d77/a0b/MD5E-s4--ec4d1eb36b22d19728e9d1d23ca84d1c.txt.log.web
new file mode 100644
index 0000000..8ef0f1f
--- /dev/null
+++ b/d77/a0b/MD5E-s4--ec4d1eb36b22d19728e9d1d23ca84d1c.txt.log.web
@@ -0,0 +1 @@
+1719758896s 1 :dl+archive:MD5E-s3584--2f350c3650d5e3a21785d55f5a94ce70.tar#path=1/file.txt&size=4
diff --git a/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log b/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log
new file mode 100644
index 0000000..cc638db
--- /dev/null
+++ b/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log
@@ -0,0 +1,2 @@
+1719758896s 1 c04eb54b-4b4e-5755-8436-866b043170fa
+1719758897s 0 d53ab0e3-21a9-4084-806f-bf9f5812f34e
diff --git a/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log.web b/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log.web
new file mode 100644
index 0000000..30bb5e9
--- /dev/null
+++ b/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log.web
@@ -0,0 +1 @@
+1719758896s 1 :dl+archive:MD5E-s3584--2f350c3650d5e3a21785d55f5a94ce70.tar#path=1/1.dat&size=5
```
</details>
<details>
<summary>now we got two</summary>
```shell
Author: DataLad Tester <test@example.com>
Date: Sun Jun 30 10:45:12 2024 -0400
update
diff --git a/d77/a0b/MD5E-s4--ec4d1eb36b22d19728e9d1d23ca84d1c.txt.log b/d77/a0b/MD5E-s4--ec4d1eb36b22d19728e9d1d23ca84d1c.txt.log
new file mode 100644
index 0000000..97acf53
--- /dev/null
+++ b/d77/a0b/MD5E-s4--ec4d1eb36b22d19728e9d1d23ca84d1c.txt.log
@@ -0,0 +1,2 @@
+1719758713s 0 86661c7b-0604-49e7-8d65-1baf4ca9f469
+1719758712s 1 c04eb54b-4b4e-5755-8436-866b043170fa
diff --git a/d77/a0b/MD5E-s4--ec4d1eb36b22d19728e9d1d23ca84d1c.txt.log.web b/d77/a0b/MD5E-s4--ec4d1eb36b22d19728e9d1d23ca84d1c.txt.log.web
new file mode 100644
index 0000000..e5bafba
--- /dev/null
+++ b/d77/a0b/MD5E-s4--ec4d1eb36b22d19728e9d1d23ca84d1c.txt.log.web
@@ -0,0 +1 @@
+1719758712s 1 :dl+archive:MD5E-s3584--de6498c9ca26fee011f289f5f5972ed0.tar#path=1/file.txt&size=4
diff --git a/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log b/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log
index 11934b6..97acf53 100644
--- a/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log
+++ b/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log
@@ -1,2 +1,2 @@
-1719758712s 1 86661c7b-0604-49e7-8d65-1baf4ca9f469
+1719758713s 0 86661c7b-0604-49e7-8d65-1baf4ca9f469
1719758712s 1 c04eb54b-4b4e-5755-8436-866b043170fa
commit 8c4fdbadb4b1735cbb47f833ef99235790b8bcbf
Author: DataLad Tester <test@example.com>
Date: Sun Jun 30 10:45:12 2024 -0400
update
diff --git a/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log b/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log
new file mode 100644
index 0000000..11934b6
--- /dev/null
+++ b/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log
@@ -0,0 +1,2 @@
+1719758712s 1 86661c7b-0604-49e7-8d65-1baf4ca9f469
+1719758712s 1 c04eb54b-4b4e-5755-8436-866b043170fa
diff --git a/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log.web b/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log.web
new file mode 100644
index 0000000..107c66f
--- /dev/null
+++ b/f45/7f1/MD5E-s5--db87ebcba59a8c9f34b68e713c08a718.dat.log.web
@@ -0,0 +1 @@
+1719758712s 1 :dl+archive:MD5E-s3584--de6498c9ca26fee011f289f5f5972ed0.tar#path=1/1.dat&size=5
```
</details>
for the same effect. And I believe the command which triggers them is `['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'annex', 'addurl', '--with-files', '--json', '--json-error-messages', '--batch']` which before (for years?!) resulted in expected single commit.
<details>
<summary>Here is the full set of datalad logs for the steps triggering that </summary>
```shell
[DEBUG ] Determined class of decorated function: <class 'datalad.local.add_archive_content.AddArchiveContent'>
[DEBUG ] Resolved dataset to add-archive-content: /home/yoh/.tmp/datalad_temp_tree_rsua9kmg
[DEBUG ] Determined class of decorated function: <class 'datalad.core.local.status.Status'>
[DEBUG ] Resolved dataset to report status: /home/yoh/.tmp/datalad_temp_tree_rsua9kmg
[DEBUG ] Querying AnnexRepo(/home/yoh/.tmp/datalad_temp_tree_rsua9kmg).diffstatus() for paths: [PosixPath('/home/yoh/.tmp/datalad_temp_tree_rsua9kmg/subdir/1.tar')]
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'rev-parse', '--quiet', '--verify', 'HEAD^{commit}'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] AnnexRepo(/home/yoh/.tmp/datalad_temp_tree_rsua9kmg).get_content_info(...)
[DEBUG ] Query repo: ['ls-files', '--stage', '-z', '--exclude-standard', '-o', '--directory', '--no-empty-directory']
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'ls-files', '--stage', '-z', '--exclude-standard', '-o', '--directory', '--no-empty-directory', '--', 'subdir/1.tar'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] Done query repo: ['ls-files', '--stage', '-z', '--exclude-standard', '-o', '--directory', '--no-empty-directory']
[DEBUG ] Done AnnexRepo(/home/yoh/.tmp/datalad_temp_tree_rsua9kmg).get_content_info(...)
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'ls-files', '-z', '-m', '-d', '--', 'subdir/1.tar'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] AnnexRepo(/home/yoh/.tmp/datalad_temp_tree_rsua9kmg).get_content_info(...)
[DEBUG ] Query repo: ['ls-tree', 'HEAD', '-z', '-r', '--full-tree', '-l']
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'ls-tree', 'HEAD', '-z', '-r', '--full-tree', '-l', '--', 'subdir/1.tar'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] Done query repo: ['ls-tree', 'HEAD', '-z', '-r', '--full-tree', '-l']
[DEBUG ] Done AnnexRepo(/home/yoh/.tmp/datalad_temp_tree_rsua9kmg).get_content_info(...)
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'status', '--porcelain', '--untracked-files=normal', '--ignore-submodules=none'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'annex', 'find', '--anything', '--json', '--json-error-messages', '-c', 'annex.dotfiles=true', '--', 'subdir/1.tar'] (protocol_class=AnnexJsonProtocol) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] Finished ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'annex', 'find', '--anything', '--json', '--json-error-messages', '-c', 'annex.dotfiles=true', '--', 'subdir/1.tar'] with status 0
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'annex', 'contentlocation', 'MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar', '-c', 'annex.dotfiles=true'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[INFO ] Adding content of the archive subdir/1.tar into annex AnnexRepo(/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] Initiating clean cache for the archives under /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/datalad/tmp/archives
[DEBUG ] Cache initialized
[DEBUG ] Not initiating existing cache for the archives under /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/datalad/tmp/archives
[DEBUG ] Cached directory for archive /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/annex/objects/gg/zf/MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar/MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar is fbab09b98e
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'cat-file', 'blob', 'git-annex:remote.log'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[Level 11] CommandError: 'git -c diff.ignoreSubmodules=none -c core.quotepath=false cat-file blob git-annex:remote.log' failed with exitcode 128 [err: 'fatal: path 'remote.log' does not exist in 'git-annex'']
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'cat-file', 'blob', 'git-annex:trust.log'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[Level 11] CommandError: 'git -c diff.ignoreSubmodules=none -c core.quotepath=false cat-file blob git-annex:trust.log' failed with exitcode 128 [err: 'fatal: path 'trust.log' does not exist in 'git-annex'']
[INFO ] Initializing special remote datalad-archives
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'annex', 'initremote', 'datalad-archives', 'encryption=none', 'type=external', 'autoenable=true', 'externaltype=datalad-archives', 'uuid=c04eb54b-4b4e-5755-8436-866b043170fa', '-c', 'annex.dotfiles=true'] (protocol_class=StdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] Finished ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'annex', 'initremote', 'datalad-archives', 'encryption=none', 'type=external', 'autoenable=true', 'externaltype=datalad-archives', 'uuid=c04eb54b-4b4e-5755-8436-866b043170fa', '-c', 'annex.dotfiles=true'] with status 0
[DEBUG ] Run ['git', 'config', '-z', '-l', '--show-origin'] (protocol_class=StdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] Finished ['git', 'config', '-z', '-l', '--show-origin'] with status 0
[DEBUG ] Acquiring a lock /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/datalad/tmp/archives/fbab09b98e.extract-lck
[DEBUG ] Acquired? lock /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/datalad/tmp/archives/fbab09b98e.extract-lck: True
[DEBUG ] Extracting /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/annex/objects/gg/zf/MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar/MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar under /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/datalad/tmp/archives/fbab09b98e
[DEBUG ] Run ['7z', 'x', '/home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/annex/objects/gg/zf/MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar/MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar'] (protocol_class=KillOutput) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/datalad/tmp/archives/fbab09b98e)
[DEBUG ] Finished ['7z', 'x', '/home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/annex/objects/gg/zf/MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar/MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar'] with status 0
[DEBUG ] Releasing lock /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/datalad/tmp/archives/fbab09b98e.extract-lck
[INFO ] Start Extracting archive
[DEBUG ] Adding /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/subdir/.dataladiwgxvqzi/1/1.dat to annex pointing to dl+archive:MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar#path=1/1.dat&size=5 and with options None
[DEBUG ] Starting new runner for BatchedAnnex(command=['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'annex', 'addurl', '--with-files', '--json', '--json-error-messages', '--batch'], encoding=None, exception_on_timeout=False, last_request=None, output_proc=<function readline_json at 0x7f165f5adf80>, path=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg, return_code=None, runner=None, stderr_output=b'', timeout=None, wait_timed_out=None)
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'annex', 'addurl', '--with-files', '--json', '--json-error-messages', '--batch'] (protocol_class=BatchedCommandProtocol) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] Starting new runner for BatchedAnnex(command=['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'annex', 'dropkey', '--force', '--json', '--json-error-messages', '--batch'], encoding=None, exception_on_timeout=False, last_request=None, output_proc=<function readline_json at 0x7f165f5adf80>, path=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg, return_code=None, runner=None, stderr_output=b'', timeout=None, wait_timed_out=None)
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'annex', 'dropkey', '--force', '--json', '--json-error-messages', '--batch'] (protocol_class=BatchedCommandProtocol) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] Adding /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/subdir/.dataladiwgxvqzi/1/file.txt to annex pointing to dl+archive:MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar#path=1/file.txt&size=4 and with options None
[INFO ] Finished adding subdir/1.tar: Files processed: 2, renamed: 2, removed: 2, +annex: 2
[DEBUG ] Removing extracted and annexed files under /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/subdir/.dataladiwgxvqzi
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'rm', '--force', '-r', '--', 'subdir/.dataladiwgxvqzi'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] Query status of AnnexRepo('/home/yoh/.tmp/datalad_temp_tree_rsua9kmg') for all paths
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'rev-parse', '--quiet', '--verify', 'HEAD^{commit}'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] AnnexRepo(/home/yoh/.tmp/datalad_temp_tree_rsua9kmg).get_content_info(...)
[DEBUG ] Query repo: ['ls-files', '--stage', '-z']
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'ls-files', '--stage', '-z'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] Done query repo: ['ls-files', '--stage', '-z']
[DEBUG ] Done AnnexRepo(/home/yoh/.tmp/datalad_temp_tree_rsua9kmg).get_content_info(...)
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'ls-files', '-z', '-m', '-d'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] AnnexRepo(/home/yoh/.tmp/datalad_temp_tree_rsua9kmg).get_content_info(...)
[DEBUG ] Query repo: ['ls-tree', 'HEAD', '-z', '-r', '--full-tree', '-l']
[DEBUG ] Run ['git', '-c', 'diff.ignoreSubmodules=none', '-c', 'core.quotepath=false', 'ls-tree', 'HEAD', '-z', '-r', '--full-tree', '-l'] (protocol_class=GeneratorStdOutErrCapture) (cwd=/home/yoh/.tmp/datalad_temp_tree_rsua9kmg)
[DEBUG ] Done query repo: ['ls-tree', 'HEAD', '-z', '-r', '--full-tree', '-l']
[DEBUG ] Done AnnexRepo(/home/yoh/.tmp/datalad_temp_tree_rsua9kmg).get_content_info(...)
[INFO ] Extracting archive 2 Files done in 0.872975 sec at 2.29102 Files/sec
[DEBUG ] Cleaning up the cache for /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/annex/objects/gg/zf/MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar/MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar under /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/datalad/tmp/archives/fbab09b98e
[DEBUG ] Cleaning up the stamp file for /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/annex/objects/gg/zf/MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar/MD5E-s3584--bb87b72d411b7415410da27950d2a165.tar under /home/yoh/.tmp/datalad_temp_tree_rsua9kmg/.git/datalad/tmp/archives/fbab09b98e.stamp
add-archive-content(ok): /home/yoh/.tmp/datalad_temp_tree_rsua9kmg (dataset)
```
</details>
[[!meta author=yoh]]
[[!tag projects/repronim]]

92
doc/bugs/keeps_trying_to_commit_file_unlocked.mdwn Normal file
View file

@ -0,0 +1,92 @@
### Please describe the problem.
I do not remember trying to add that file "unlocked" anyhow, but git-annex, upon 2nd invocation of `git status` flips the file claiming it should get to the "unlocked" git link from original symlink:
```
❯ git annex version
git-annex version: 10.20240531+git214-g28f5c47b5a-1~ndall+1
❯ git status
On branch master
Your branch is ahead of 'origin/master' by 1 commit.
(use "git push" to publish your local commits)
Changes not staged for commit:
(use "git add <file>..." to update what will be committed)
(use "git restore <file>..." to discard changes in working directory)
modified: samples/UK_gla_3T_fMRI_consent_form_v3.0.docx
no changes added to commit (use "git add" and/or "git commit -a")
❯ git reset --hard
HEAD is now at 8700315 BF: fix leftover merge conflict in CONTRIBUTING.rst
```
so here from a clean state on first `git status` we get to dirty on subsequent:
```
❯ git status
git-annex: git status will show samples/UK_gla_3T_fMRI_consent_form_v3.0.docx to be modified, since content availability has changed and git-annex was unable to update the index. This is only a cosmetic problem affecting git status; git add, git commit, etc won't be affected. To fix the git status display, you can run: git-annex restage
On branch master
Your branch is ahead of 'origin/master' by 1 commit.
(use "git push" to publish your local commits)
nothing to commit, working tree clean
❯ git status
On branch master
Your branch is ahead of 'origin/master' by 1 commit.
(use "git push" to publish your local commits)
Changes not staged for commit:
(use "git add <file>..." to update what will be committed)
(use "git restore <file>..." to discard changes in working directory)
modified: samples/UK_gla_3T_fMRI_consent_form_v3.0.docx
no changes added to commit (use "git add" and/or "git commit -a")
❯ git diff
diff --git a/samples/UK_gla_3T_fMRI_consent_form_v3.0.docx b/samples/UK_gla_3T_fMRI_consent_form_v3.0.docx
index 3215574..488e63f 100644
--- a/samples/UK_gla_3T_fMRI_consent_form_v3.0.docx
+++ b/samples/UK_gla_3T_fMRI_consent_form_v3.0.docx
@@ -1 +1 @@
-../.git/annex/objects/5M/wv/MD5E-s591826--1ca9251906259623f73a3aba47ef6369.0.docx/MD5E-s591826--1ca9251906259623f73a3aba47ef6369.0.docx
\ No newline at end of file
+/annex/objects/MD5E-s591826--1ca9251906259623f73a3aba47ef6369.0.docx
❯ git annex restage
restage ok
❯ git diff
❯ git status
On branch master
Your branch is ahead of 'origin/master' by 1 commit.
(use "git push" to publish your local commits)
Changes to be committed:
(use "git restore --staged <file>..." to unstage)
modified: samples/UK_gla_3T_fMRI_consent_form_v3.0.docx
❯ git diff --cached
diff --git a/samples/UK_gla_3T_fMRI_consent_form_v3.0.docx b/samples/UK_gla_3T_fMRI_consent_form_v3.0.docx
index 3215574..488e63f 100644
--- a/samples/UK_gla_3T_fMRI_consent_form_v3.0.docx
+++ b/samples/UK_gla_3T_fMRI_consent_form_v3.0.docx
@@ -1 +1 @@
-../.git/annex/objects/5M/wv/MD5E-s591826--1ca9251906259623f73a3aba47ef6369.0.docx/MD5E-s591826--1ca9251906259623f73a3aba47ef6369.0.docx
\ No newline at end of file
+/annex/objects/MD5E-s591826--1ca9251906259623f73a3aba47ef6369.0.docx
```
This is on a local long-lived clone of http://github.com/con/open-brain-consent but seems to not happen on a fresh clone. So must be something about local "state".
Not sure if relates to the following issue under current investigation (but not yet addressed):
- [https://git-annex.branchable.com/bugs/assistant___40__webapp__41___commited_unlocked_link_to_annex/](https://git-annex.branchable.com/bugs/assistant___40__webapp__41___commited_unlocked_link_to_annex/)
[[!meta author=yoh]]
[[!tag projects/repronim]]