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### Please describe the problem.
On Windows 7, the committed symlink files are always relative to the repo's .git root; they are not prefixed with the correct number of ../ for the given level of directing nesting.
Trying to correct this with `git annex fix` returns "You cannot run this command in a direct mode repository."
I believe that this is also the source of a pathological case I'm seeing on Windows. After adding a lot of content, commands like `git annex sync` and `git annex status` appear to re-checksum the entire annex. After syncing the repo to a Linux machine, fixing the symlinks there, and syncing back, these commands become snappy again.
### What steps will reproduce the problem?
[[!format sh """
git init
git annex init
mkdir -p one/two/three/four/five/six
# drop files into the dir structure
git annex add .
git annex sync
git log -p
"""]]
### What version of git-annex are you using? On what operating system?
git-annex version: 5.20140203-g83e6fb7
on Windows 7 Pro
### Please provide any additional information below.
The output of `git log -p` for me:
commit f4d88b6bc99cc94a0b0154da41d06bad3f23cc1e
Author: Justin Geibel <...>
Date: Tue Feb 4 20:56:32 2014 -0500
git-annex automatic sync
diff --git a/git-annex-installer.exe b/git-annex-installer.exe
new file mode 120000
index 0000000..64f7d83
--- /dev/null
+++ b/git-annex-installer.exe
@@ -0,0 +1 @@
+.git/annex/objects/GW/Wk/SHA256E-s14413167--ea3a1e4c09ad12fdb2993a157b77b246a058f7f0ca2cd174d8cc675d1495ec4d.exe/SHA256E-s14413167--ea3a1e4c09ad12fdb2993a157b77b246a058f7f0ca2cd174d8cc675d1495ec4d.exe
\ No newline at end of file
diff --git a/one/git-annex-installer(1).exe b/one/git-annex-installer(1).exe
new file mode 120000
index 0000000..5b37a29
--- /dev/null
+++ b/one/git-annex-installer(1).exe
@@ -0,0 +1 @@
+.git/annex/objects/6k/8K/SHA256E-s19286321--add3e1ac7ceabce7aa1ed1907895ae527fc095610d1e21127e99814728b24f11.exe/SHA256E-s19286321--add3e1ac7ceabce7aa1ed1907895ae527fc095610d1e21127e99814728b24f11.exe
\ No newline at end of file
diff --git a/one/two/git-annex-installer(2).exe b/one/two/git-annex-installer(2).exe
new file mode 120000
index 0000000..f89508f
--- /dev/null
+++ b/one/two/git-annex-installer(2).exe
@@ -0,0 +1 @@
+.git/annex/objects/Zm/6K/SHA256E-s19573485--4f2a22c5b96308cf694c85564940d3cba22b5e8b3b714b242116c91369be75ee.exe/SHA256E-s19573485--4f2a22c5b96308cf694c85564940d3cba22b5e8b3b714b242116c91369be75ee.exe
\ No newline at end of file
diff --git a/one/two/three/four/five/git-annex-installer(5).exe b/one/two/three/four/five/git-annex-installer(5).exe
new file mode 120000
index 0000000..34565f9
--- /dev/null
+++ b/one/two/three/four/five/git-annex-installer(5).exe
@@ -0,0 +1 @@
+.git/annex/objects/p3/Xq/SHA256E-s19956630--ec421bfc6cb0b4df2b5195d9229cbcc27a2e5505e0b879bf07e1be38dcc64a42.exe/SHA256E-s19956630--ec421bfc6cb0b4df2b5195d9229cbcc27a2e5505e0b879bf07e1be38dcc64a42.exe
\ No newline at end of file
diff --git a/one/two/three/four/five/six/git-annex-installer(6).exe b/one/two/three/four/five/six/git-annex-installer(6).exe
new file mode 120000
index 0000000..d6f97d9
--- /dev/null
+++ b/one/two/three/four/five/six/git-annex-installer(6).exe
@@ -0,0 +1 @@
+.git/annex/objects/9G/5g/SHA256E-s19967171--c9e33dff779a43e76089ec3bee3411299d5b8abfa67ae1b459cee5a812c5194d.exe/SHA256E-s19967171--c9e33dff779a43e76089ec3bee3411299d5b8abfa67ae1b459cee5a812c5194d.exe
\ No newline at end of file
diff --git a/one/two/three/four/git-annex-installer(4).exe b/one/two/three/four/git-annex-installer(4).exe
new file mode 120000
index 0000000..a4f791c
--- /dev/null
+++ b/one/two/three/four/git-annex-installer(4).exe
@@ -0,0 +1 @@
+.git/annex/objects/8J/pM/SHA256E-s19959961--7e4521036f891bba97f4c04527946e26ef43b14576d874c666e73dee405c18cf.exe/SHA256E-s19959961--7e4521036f891bba97f4c04527946e26ef43b14576d874c666e73dee405c18cf.exe
\ No newline at end of file
diff --git a/one/two/three/git-annex-installer(3).exe b/one/two/three/git-annex-installer(3).exe
new file mode 120000
index 0000000..dda7284
--- /dev/null
+++ b/one/two/three/git-annex-installer(3).exe
@@ -0,0 +1 @@
+.git/annex/objects/5X/qQ/SHA256E-s19915186--c6dc288ec8a77404c0ebc22cbe9b4ec911103fd022c3ca74eec582604dff80a7.exe/SHA256E-s19915186--c6dc288ec8a77404c0ebc22cbe9b4ec911103fd022c3ca74eec582604dff80a7.exe
\ No newline at end of file
> [[fixed|done]] -- I didn't notice this before because it happened to do
> the right thing if you cd'd into the subdir before adding the file there.
>
> WRT the slow down issue, I don't see how it could matter to git-annex on
> Windows whether the symlinks point to the right place. It only looks at
> the basename of the symlink target to get the key. If you have a
> repository that behaves poorly, you can probably use --debug to see if
> git-annex is calling some expensive series of git commands somehow.
> --[[Joey]]
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