Ignore Sync errors on pipes when doing CheckAttributeReader.CheckPath, fix the hang of git cat-file (#17096)

* Ignore Sync errors on pipes when doing `CheckAttributeReader.CheckPath`

* apply env patch

* Drop the Sync and fix a number of issues with the Close function

Signed-off-by: Andrew Thornton <art27@cantab.net>

* add logs for DBIndexer and CheckPath

* Fix some more closing bugs

Signed-off-by: Andrew Thornton <art27@cantab.net>

* Add test case for language_stats

Signed-off-by: Andrew Thornton <art27@cantab.net>

* Update modules/indexer/stats/db.go

Co-authored-by: Lauris BH <lauris@nix.lv>

Co-authored-by: Andrew Thornton <art27@cantab.net>
Co-authored-by: Lauris BH <lauris@nix.lv>
Co-authored-by: 6543 <6543@obermui.de>

modules/git/tests/repos/language_stats_repo/hooks/push-to-checkout.sample

@@ -0,0 +1,78 @@
+#!/bin/sh
+
+# An example hook script to update a checked-out tree on a git push.
+#
+# This hook is invoked by git-receive-pack(1) when it reacts to git
+# push and updates reference(s) in its repository, and when the push
+# tries to update the branch that is currently checked out and the
+# receive.denyCurrentBranch configuration variable is set to
+# updateInstead.
+#
+# By default, such a push is refused if the working tree and the index
+# of the remote repository has any difference from the currently
+# checked out commit; when both the working tree and the index match
+# the current commit, they are updated to match the newly pushed tip
+# of the branch. This hook is to be used to override the default
+# behaviour; however the code below reimplements the default behaviour
+# as a starting point for convenient modification.
+#
+# The hook receives the commit with which the tip of the current
+# branch is going to be updated:
+commit=$1
+
+# It can exit with a non-zero status to refuse the push (when it does
+# so, it must not modify the index or the working tree).
+die () {
+	echo >&2 "$*"
+	exit 1
+}
+
+# Or it can make any necessary changes to the working tree and to the
+# index to bring them to the desired state when the tip of the current
+# branch is updated to the new commit, and exit with a zero status.
+#
+# For example, the hook can simply run git read-tree -u -m HEAD "$1"
+# in order to emulate git fetch that is run in the reverse direction
+# with git push, as the two-tree form of git read-tree -u -m is
+# essentially the same as git switch or git checkout that switches
+# branches while keeping the local changes in the working tree that do
+# not interfere with the difference between the branches.
+
+# The below is a more-or-less exact translation to shell of the C code
+# for the default behaviour for git's push-to-checkout hook defined in
+# the push_to_deploy() function in builtin/receive-pack.c.
+#
+# Note that the hook will be executed from the repository directory,
+# not from the working tree, so if you want to perform operations on
+# the working tree, you will have to adapt your code accordingly, e.g.
+# by adding "cd .." or using relative paths.
+
+if ! git update-index -q --ignore-submodules --refresh
+then
+	die "Up-to-date check failed"
+fi
+
+if ! git diff-files --quiet --ignore-submodules --
+then
+	die "Working directory has unstaged changes"
+fi
+
+# This is a rough translation of:
+#
+#   head_has_history() ? "HEAD" : EMPTY_TREE_SHA1_HEX
+if git cat-file -e HEAD 2>/dev/null
+then
+	head=HEAD
+else
+	head=$(git hash-object -t tree --stdin </dev/null)
+fi
+
+if ! git diff-index --quiet --cached --ignore-submodules $head --
+then
+	die "Working directory has staged changes"
+fi
+
+if ! git read-tree -u -m "$commit"
+then
+	die "Could not update working tree to new HEAD"
+fi