Git - Broken Links, Missing & Dangling Trees

Question

I was happily using Git - made some commits a couple of nights ago, which are reflected in the remote repo. Last night I opened up Smartgit Hg and it tells me there are missing trees. I ran git fsck --full and got the rather large output below.

I'm a Git amateur. I use a GUI to do what I need to do. I've tried reading through this (https://git.wiki.kernel.org/index.php/GitFaq#How_to_fix_a_broken_repository.3F) but it isn't making an awful lot of sense and following it blindly doesn't seem to be working.

I did a git ls-tree c957fc03bb53181547142045917211fbc380a8df and it shows me a list of files. I had 3 with a 100644 at the beginning, so I moved in to that directory, ran git hash-object -w filename and it output the same hash as the ls-tree showed me.

The wiki page says now I'm all done. Except git fsck --full still shows the same message for that tree. I get the feeling that I'm probably running these commands on the wrong thing.

I've tried reading other git posts on here, but they don't make sense to me. I won't lie.

git fsck --full
Checking object directories: 100% (256/256), done.
Checking objects: 100% (1149/1149), done.
broken link from    tree c957fc03bb53181547142045917211fbc380a8df
              to    tree e7822f570245310f4b475e043f5fb02fa45c0d9e
broken link from    tree 8005ba4728321473684e670feb9c1ada8783c007
              to    tree 4df5de19988a1fd7088da6e8214404cda2069852
broken link from    tree 3b1b915c6f306ae4f80a2b61767c4267d48df53d
              to    tree 4dc2258f8d36dbeea64b859ab5dff0fadc5bd591
broken link from    tree c850459b3bd5899bd0a9eca40d69e49582f44a19
              to    tree 912613a23bcb22f211ce0d8ab4fe2a8fddde78b6
broken link from  commit 8775851e59bd5072ab98a739cfc00b231be54eab
              to    tree 90e5f62642dde43c110b9882c564349074097955
broken link from    tree 331b16c460e6f9dd3bae9b0206857fc2c57bacb8
              to    tree fdead5b5ff4ae53b54104ab5b7fa2369f0adb4f7
broken link from    tree 3ca3d56fd7eabe9efb0d4212615cf85ced8f663f
              to    tree 099070c9c54a16ca6b78c384a43c2e45d56eed71
broken link from    tree ffe425a5a568e5e515fa5745e8dd0a3f9148ac6a
              to    tree 91ec315f9730d3541bba2603f09d69b2b6d5ead0
broken link from    tree e38aa29f31a314bf71c40d800ea9d4b9422a09c3
              to    tree b9760875bb7b8be0799435625fd686c985860de2
broken link from    tree 920755bbb97bcf526bfbd492451182bec66e6d39
              to    tree d4dcb141f4ea62228e85f6b35c5b4d2f22a8720e
broken link from    tree 298bbba4562267349db2539e43cd2f12cd4317dd
              to    tree b8234d1f9efcc9691f2b35b8e4237dfa08bc140a
broken link from  commit f106420cddf314c6efa2e015e348006b82cd6348
              to    tree a5b976cb4f82b339f22c74811f47ad31d353764b
broken link from  commit 5968e9e1479fdbba079ab64a6171f98b0f869b41
              to    tree 64171c569ea7f74f59dc8f3dcc957220aa09f343
broken link from  commit c54b5f446988645caf935382ea7bbc7ec57092f2
              to    tree fda728fd6e61790133f15e073335e2e6c43dc31b
broken link from  commit 37a6d43e9645873ab2315e641ef8bf55afc08012
              to    tree 90c19ab5f9cb64e40cfcad2e30e1cf98ad586502
broken link from    tree 32009a6e84fd8639b411433d13bb707ed25a8992
              to    tree 691f8fac71c39b2182acf51f56ac39c4bc4759d5
broken link from    tree 41db7d6238919ea58c2c64d9f333c63650e0e95a
              to    tree 649a4fc0f5a9d06c67223a36116c7c8aeaa2c6b9
broken link from    tree 84f823c8d4032a3fe09ba4d962603fcb975dbf98
              to    tree 7bb4a11dd10def2f1f4f9bae4eea02848fb833cb
broken link from  commit 1b85354dd48be428b4d3937da24a9951efa9f451
              to    tree 3d437dcff812a0e123d2e4b741dba47ad08a6b9e
broken link from  commit 2cbfbe123e1a61584c519f190015622ae5b5c8c0
              to    tree 0013af31f091e2d22b7ff7e63badf305597e63b4
broken link from    tree fef036d59eb8944bb494a0eff85325c108fccf34
              to    tree 896deb89905c80893512a61d9f8e9fc3760f3a53
broken link from    tree f26d568cf61282aa1f04e7828bddf8f9d7cf8ecb
              to    tree 3d7994b9dad00c47c64b99e30693c0215b0aa5eb
broken link from    tree bc7d7d62d92c8989d9e398c8cbf036f1e205f855
              to    tree ea29c58710d7d3aa7cce589de9b46503d0e9565e
broken link from    tree 447585f3684b9915ba0ce99f41359da197ee8f54
              to    tree 0992afc3aa3aa332fe3dc927a5e334f69638a898
broken link from  commit 5e622e95cb5336521cbbdb7c03b860bb74eb9f8c
              to    tree 7f91438587057ac610e44a5cf3318440e004a9bc
broken link from    tree 32f13f592d0a56d467234b838930039c0438e019
              to    tree 9d3328f820a9308bab950ee9e513a200acd6d3f4
missing tree 099070c9c54a16ca6b78c384a43c2e45d56eed71
dangling tree 5a0069463363b395881958eb8d9aac7ba1b9ddd8
dangling tree 932053ef04d4f540d250d5e74332d141b4037009
dangling tree c7a04a22febdeb307f38019aff2e4f7645a7ea9f
dangling tree cf10f1a8c2bb57520c6e0ad256e9fb344961c13a
dangling tree 2c51ad373aef4844fc9e6babd878dfae5f5592b3
missing tree 7f91438587057ac610e44a5cf3318440e004a9bc
missing tree 90c19ab5f9cb64e40cfcad2e30e1cf98ad586502
missing tree 0992afc3aa3aa332fe3dc927a5e334f69638a898
dangling blob 24226e3db997d21dc10aa70a9a8aa279aa55fb8a
missing tree 4dc2258f8d36dbeea64b859ab5dff0fadc5bd591
dangling tree 9c322d15436be34a99fcea442ad97ae40715ac61
dangling tree b4d2505972386aba42282232843d4e1b73148be4
missing tree e7822f570245310f4b475e043f5fb02fa45c0d9e
missing tree 0013af31f091e2d22b7ff7e63badf305597e63b4
missing blob 35e3ddbc07214e74d8ad516736ee0e90b0a285c8
missing tree 3d437dcff812a0e123d2e4b741dba47ad08a6b9e
dangling tree 6d637bdae8eff5490df307fce3fd8a1bb2e5ce14
dangling tree 79934929fc8423ec1c277ab21d14b7434cde7544
missing tree 9d3328f820a9308bab950ee9e513a200acd6d3f4
missing tree b8234d1f9efcc9691f2b35b8e4237dfa08bc140a
dangling tree d1333fd1a2c9fed8bc3cc6f58ae00bf7fbe7c482
missing blob 20149c8fb22e309a26f477f0e500e122f6e99e66
dangling tree 4054641b41208cc98387806a877855db15a109f9
missing tree 7bb4a11dd10def2f1f4f9bae4eea02848fb833cb
dangling tree f4948b5302a1fe79ea09c5959e0f3902d022a2b3
missing tree 4df5de19988a1fd7088da6e8214404cda2069852
missing tree 90e5f62642dde43c110b9882c564349074097955
dangling tree 7966c4a2fc16a5559b569f5e200c0f01f0b186db
missing tree 912613a23bcb22f211ce0d8ab4fe2a8fddde78b6
missing commit b976d2df1880cb6c90db5bdf856440904cd22574
missing tree b9760875bb7b8be0799435625fd686c985860de2
missing commit 35e7e9f65cf5950ae2855afaf764672dd48a8b9b
missing tree 64171c569ea7f74f59dc8f3dcc957220aa09f343
missing tree fda728fd6e61790133f15e073335e2e6c43dc31b
dangling tree 29088a01bfe6bde49cf1176b7ed1171dd8f8e334
missing commit e27876491d426b8d9f3932eb2ee494145f8776b5
dangling tree e3c8535db10a99db65fbd5c2e58e2c3b59159d24
missing tree 3d7994b9dad00c47c64b99e30693c0215b0aa5eb
dangling tree 6129fef595c71128c0dc24ebd4248ef231cfe90d
missing tree a5b976cb4f82b339f22c74811f47ad31d353764b
missing tree ea29c58710d7d3aa7cce589de9b46503d0e9565e
missing tree 649a4fc0f5a9d06c67223a36116c7c8aeaa2c6b9
missing commit 8f2ad8d3aaccfcfad8cd7c30ea938008378591fd
missing blob ea1ae4f5cd2a6ec1e9982108cdbce7de5858d0d9
dangling tree f69a44eac9426e3fcfb4eb1545c966beb72b37b0
missing tree fdead5b5ff4ae53b54104ab5b7fa2369f0adb4f7
missing commit a69b6f1a1b224b2ba846590d6ddd65ca0079a1bb
missing blob 453c02a0bbce4748a3e3d3da4c29498cbf4b01d0
missing tree 91ec315f9730d3541bba2603f09d69b2b6d5ead0
missing tree d4dcb141f4ea62228e85f6b35c5b4d2f22a8720e
missing tree 896deb89905c80893512a61d9f8e9fc3760f3a53
dangling tree deeec6312c058722ffcf1b5cf14d997c14890eb1
dangling blob 0b7fc81faf339d77c2146f406a9f90c4431da4e2
missing tree 691f8fac71c39b2182acf51f56ac39c4bc4759d5
missing blob 7fef3c0e58d6c2825703576b3ecb148040e2b0cf
dangling tree 95cf9c35987a0b715d4f736d2cf9dacf82c958ae
dangling tree ce4feefca69bd3fbc82205c4c3f1c116f73b623c

Deputy

Try cloning the remote repository into a new folder. Does it also have these errors? If not, simply use this clone and delete the corrupted one. – Saltwater

I cloned. It does not have errors. I'll probably try this anyway, but is it safe to just copy the folders (not the .git folder?) from my 'working directory' to the newly cloned directory? – Deputy

If you want to put your comment as an answer I'll accept. I moved my changed files from one directory to the other and it has recognised that I have pending. Seems to be OK now. Thanks for your help. – Deputy

With Git 2.10, git fsck --name-objects can help too. See my answer here. – Saraann

Answer 1

Try cloning the remote repository into a new folder.
Does it also have these errors? If not, simply use this clone and delete the corrupted one.

Any modified files that have not yet been committed can simple be copied to the new folder. Important: Don't copy the .git folder.

Saltwater

I remember when I used to not search stackoverflow first, try out git commands I never heard of for hours and then give up on everything. ah the simplest solutions are indeed the sweetest! – Serinaserine

Answer 2

For me, a simple git gc did the job... This gave me a couple of rm: cannot unlink ... Permission denied messages. But in the end, it seemed to have worked for my case.

But probably depends on how exactly the repo is corrupted.

Enciso

Thanks, this rescued my repo after a rebase gone bad. Although making a backup of the repo would be a good idea first just in case the GC garbage collects your commits out of existence. – Bypath