Avoid converting .git file in a worktree or submodule to a symlink when the repository is not a git-annex repository.

This means it will still be a .git file when git-annex init runs. That's
ok, the repo probably contains no annexed objects yet, and even if it does,
git-annex init does not care if symlinks in the worktree don't point to the
objects.

I made init, at the end, run the conversion code. Not really necessary
because the next git-annex command could do it just as well. But, this
avoids commands that don't normally write to the repo needing to write to
it, which might avoid some problem or other, and seems worth avoiding
generally.

Annex/Fixup.hs

@@ -1,6 +1,6 @@
 {- git-annex repository fixups
  -
- - Copyright 2013-2019 Joey Hess <id@joeyh.name>
+ - Copyright 2013-2020 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -12,8 +12,6 @@ module Annex.Fixup where
 import Git.Types
 import Git.Config
 import Types.GitConfig
-import Config.Files
-import qualified Git
 import Utility.Path
 import Utility.SafeCommand
 import Utility.Directory
@@ -86,24 +84,21 @@ fixupDirect r = r
  - into a symlink. But we don't need too, since the repo will use adjusted
  - unlocked branches.
  -
- - Before making any changes, check if there's a .noannex file
- - in the repo. If that file will prevent git-annex from being used,
- - there's no need to fix up the repository.
+ - Don't do any of this if the repo has not been initialized for git-annex
+ - use yet.
  -}
 fixupUnusualRepos :: Repo -> GitConfig -> IO Repo
 fixupUnusualRepos r@(Repo { location = l@(Local { worktree = Just w, gitdir = d }) }) c
-	| needsSubmoduleFixup r = ifM notnoannex
-		( do
-			when (coreSymlinks c) $
-				(replacedotgit >> unsetcoreworktree)
-					`catchNonAsync` \_e -> hPutStrLn stderr
-						"warning: unable to convert submodule to form that will work with git-annex"
-			return $ r'
-				{ config = M.delete "core.worktree" (config r)
-				}
-		, return r
-		)
-	| otherwise = ifM (needsGitLinkFixup r <&&> notnoannex)
+	| isNothing (annexVersion c) = return r
+	| needsSubmoduleFixup r = do
+		when (coreSymlinks c) $
+			(replacedotgit >> unsetcoreworktree)
+				`catchNonAsync` \_e -> hPutStrLn stderr
+					"warning: unable to convert submodule to form that will work with git-annex"
+		return $ r'
+			{ config = M.delete "core.worktree" (config r)
+			}
+	| otherwise = ifM (needsGitLinkFixup r)
 		( do
 			when (coreSymlinks c) $
 				(replacedotgit >> worktreefixup)
@@ -144,8 +139,6 @@ fixupUnusualRepos r@(Repo { location = l@(Local { worktree = Just w, gitdir = d
 	r'
 		| coreSymlinks c = r { location = l { gitdir = dotgit } }
 		| otherwise = r
-
-	notnoannex = isNothing <$> noAnnexFileContent (fmap fromRawFilePath (Git.repoWorkTree r))
 fixupUnusualRepos r _ = return r
 
 needsSubmoduleFixup :: Repo -> Bool

Annex/Init.hs

@@ -34,6 +34,7 @@ import Annex.Version
 import Annex.Difference
 import Annex.UUID
 import Annex.WorkTree
+import Annex.Fixup
 import Config
 import Config.Files
 import Config.Smudge
@@ -129,6 +130,7 @@ initialize' mversion = checkCanInitialize  $ do
 				)
 	propigateSecureHashesOnly
 	createInodeSentinalFile False
+	fixupUnusualReposAfterInit
 
 uninitialize :: Annex ()
 uninitialize = do
@@ -280,3 +282,8 @@ propigateSecureHashesOnly :: Annex ()
 propigateSecureHashesOnly =
 	maybe noop (setConfig "annex.securehashesonly" . fromConfigValue)
 		=<< getGlobalConfig "annex.securehashesonly"
+
+fixupUnusualReposAfterInit :: Annex ()
+fixupUnusualReposAfterInit = do
+	gc <- Annex.getGitConfig
+	void $ inRepo $ \r -> fixupUnusualRepos r gc

CHANGELOG

@@ -20,8 +20,8 @@ git-annex (8.20200227) UNRELEASED; urgency=medium
   * git-annex config: Only allow configs be set that are ones git-annex actually
     supports reading from repo-global config, to avoid confusion.
   * Linux standalone: Use md5sum to shorten paths in .cache/git-annex/locales
-  * Fix a problem in auto-upgrade of a clone to v8 that caused a
-    message "fatal: <path> is outside repository".
+  * Avoid converting .git file in a worktree or submodule to a symlink
+    when the repository is not a git-annex repository.
 
  -- Joey Hess <id@joeyh.name>  Thu, 27 Feb 2020 00:44:11 -0400
 

doc/bugs/running_git_annex_commands_in_worktree_of_a_non-git-annex_repo_changes_the_.git.mdwn

@@ -65,3 +65,4 @@ Linux ip-172-31-80-211.ec2.internal 4.14.171-136.231.amzn2.x86_64 #1 SMP Thu Feb
 ### 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)
 
 
+> [[fixed|done]] --[[Joey]]

doc/bugs/running_git_annex_commands_in_worktree_of_a_non-git-annex_repo_changes_the_.git/comment_1_d5d8754af32ac45cd6303805bfe99911._comment

@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 1"""
+ date="2020-03-09T18:31:46Z"
+ content="""
+Hmm, fixupUnusualRepos was earlier changed to check for .noannex
+files, and avoid doing anything. Didn't think big enough I suppose.
+
+I agree, git-annex should not be hacking on git repos that have not had
+git-annex initialized in them yet. Luckily all the hacks are about making
+.git files into symlinks so links to annexed files work, so it will be ok
+for the .git file to remain unconverted until the end of git-annex init,
+or even by a subsequent git-annex command.
+"""]]