So this is mystifying, because this happens for only a single repo out of many that sync between two machines with the git-annex assistant. All other repos sync successfully.

Updating fb9c1a7..e5b6add
git-annex filter-process: git-annex: command not found
fatal: the remote end hung up unexpectedly

  realpath: does not exist (No such file or directory)

Outbound config:

[core]
    repositoryformatversion = 0
    filemode = true
    bare = false
    logallrefupdates = true
    ignorecase = true
    precomposeunicode = true
[remote "mini"]
    url = me@mini:Self/repos/trading-obsidian
    fetch = +refs/heads/*:refs/remotes/mini/*
    annex-uuid = xxxx
[branch "master"]
    remote = mini
    merge = refs/heads/master
[annex]
    uuid = xxxx
    version = 10
[filter "annex"]
    smudge = git-annex smudge -- %f
    clean = git-annex smudge --clean -- %f
    process = git-annex filter-process

I can ssh in and run commands:

ssh -A mini 'git-annex version'
git-annex version: 10.20241202
build flags: Assistant Webapp Pairing FsEvents TorrentParser MagicMime Servant Benchmark Feeds Testsuite S3 WebDAV
dependency versions: aws-0.24.3 bloomfilter-2.0.1.2 crypton-1.0.1 DAV-1.3.4 feed-1.3.2.1 ghc-9.8.2 http-client-0.7.17 persistent-sqlite-2.13.3.0 torrent-10000.1.3 uuid-1.3.16 yesod-1.6.2.1
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2BP512E BLAKE2BP512 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL GITBUNDLE GITMANIFEST VURL X*
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar git-lfs httpalso borg rclone hook external
operating system: darwin x86_64
supported repository versions: 8 9 10
upgrade supported from repository versions: 0 1 2 3 4 5 6 7 8 9 10

ssh -A mini 'which git-annex-shell'
/Users/me/bin/git-annex-shell

I didn't intentionally configure this repo any differently than any other repo.

For example, the assistant doesn't emit this error for another repo on the same source machine, although I have no idea what a realpath is and why this happens in every repo, but this error doesn't seem to be causing the problem.

Updating 4963189..4055a92
Fast-forward
 file.md | 2 ++
 1 file changed, 2 insertions(+)

  realpath: does not exist (No such file or directory)
ssh: connect to host mini port 22: Operation timed out

  realpath: does not exist (No such file or directory)
ssh: connect to host mini port 22: Operation timed out

  realpath: does not exist (No such file or directory)
ssh: connect to host mini port 22: Operation timed out

  realpath: does not exist (No such file or directory)
ssh: connect to host mini port 22: Operation timed out
ssh: connect to host mini port 22: Operation timed out

  realpath: does not exist (No such file or directory)

Any suggestions are appreciated, thanks!