Init.checkCanInitialize aborts if it finds a ".noannex" file, but before doing so Annex.new runs fixupRepo. This results in the .git file being unnecessarily converted to a symlink. It's minor, but it'd be nice if git-annex avoided touching the repo in this situation because git treats the symlink differently than the .git file in some ways. For example, in the case of worktrees, trying to remove a fixed up one will fail:

% git worktree remove ../wt
fatal: validation failed, cannot remove working tree: '/tmp/tmp.Z0NByT6PLO/wt/.git' is not a .git file, error code 2

Here's a demo of the issue:

% git init main
% cd main
% touch .noannex
% git add .noannex
% git commit -mnoannex
% git worktree add ../wt HEAD
% cd ../wt

% ls -l .git
-rw-r--r-- 1 kyle kyle 51 Jan 29 10:58 .git
% cat .git
gitdir: /tmp/tmp.Z0NByT6PLO/main/.git/worktrees/wt

% git annex init
init  
  Initialization prevented by .noannex file (use --force to override)

git-annex: Not initialized.
failed
git-annex: init: 1 failed

% ls -l .git
lrwxrwxrwx 1 kyle kyle 25 Jan 29 10:58 .git -> ../main/.git/worktrees/wt

% git annex version
git-annex version: 7.20181121+git58-gbc4aa3f0e-1~ndall+1
build flags: Assistant Webapp Pairing S3(multipartupload)(storageclasses) WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
dependency versions: aws-0.20 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.3 feed-1.0.0.0 ghc-8.4.3 http-client-0.5.13.1 persistent-sqlite-2.8.2 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.0
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 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar hook external
operating system: linux x86_64
supported repository versions: 5 7
upgrade supported from repository versions: 0 1 2 3 4 5 6

fixed --Joey