diff --git a/alias.c b/alias.c
index 3b90397a99..0526304661 100644
--- a/alias.c
+++ b/alias.c
@@ -1,14 +1,28 @@
 #include "cache.h"
 
+struct config_alias_data {
+	const char *alias;
+	char *v;
+};
+
+static int config_alias_cb(const char *key, const char *value, void *d)
+{
+	struct config_alias_data *data = d;
+	const char *p;
+
+	if (skip_prefix(key, "alias.", &p) && !strcmp(p, data->alias))
+		return git_config_string((const char **)&data->v, key, value);
+
+	return 0;
+}
+
 char *alias_lookup(const char *alias)
 {
-	char *v = NULL;
-	struct strbuf key = STRBUF_INIT;
-	strbuf_addf(&key, "alias.%s", alias);
-	if (git_config_key_is_valid(key.buf))
-		git_config_get_string(key.buf, &v);
-	strbuf_release(&key);
-	return v;
+	struct config_alias_data data = { alias, NULL };
+
+	read_early_config(config_alias_cb, &data);
+
+	return data.v;
 }
 
 #define SPLIT_CMDLINE_BAD_ENDING 1
diff --git a/config.c b/config.c
index 34a139c40b..547daf87d4 100644
--- a/config.c
+++ b/config.c
@@ -604,7 +604,8 @@ static int get_value(config_fn_t fn, void *data, struct strbuf *name)
 	 */
 	cf->linenr--;
 	ret = fn(name->buf, value, data);
-	cf->linenr++;
+	if (ret >= 0)
+		cf->linenr++;
 	return ret;
 }
 
diff --git a/git.c b/git.c
index 1b8b7f51a6..6150d6d281 100644
--- a/git.c
+++ b/git.c
@@ -16,53 +16,9 @@ const char git_more_info_string[] =
 	   "to read about a specific subcommand or concept.");
 
 static int use_pager = -1;
-static char *orig_cwd;
-static const char *env_names[] = {
-	GIT_DIR_ENVIRONMENT,
-	GIT_WORK_TREE_ENVIRONMENT,
-	GIT_IMPLICIT_WORK_TREE_ENVIRONMENT,
-	GIT_PREFIX_ENVIRONMENT
-};
-static char *orig_env[4];
-static int save_restore_env_balance;
 
 static void list_builtins(void);
 
-static void save_env_before_alias(void)
-{
-	int i;
-
-	assert(save_restore_env_balance == 0);
-	save_restore_env_balance = 1;
-	orig_cwd = xgetcwd();
-	for (i = 0; i < ARRAY_SIZE(env_names); i++) {
-		orig_env[i] = getenv(env_names[i]);
-		orig_env[i] = xstrdup_or_null(orig_env[i]);
-	}
-}
-
-static void restore_env(int external_alias)
-{
-	int i;
-
-	assert(save_restore_env_balance == 1);
-	save_restore_env_balance = 0;
-	if (!external_alias && orig_cwd && chdir(orig_cwd))
-		die_errno("could not move to %s", orig_cwd);
-	free(orig_cwd);
-	for (i = 0; i < ARRAY_SIZE(env_names); i++) {
-		if (external_alias &&
-		    !strcmp(env_names[i], GIT_PREFIX_ENVIRONMENT))
-			continue;
-		if (orig_env[i]) {
-			setenv(env_names[i], orig_env[i], 1);
-			free(orig_env[i]);
-		} else {
-			unsetenv(env_names[i]);
-		}
-	}
-}
-
 static void commit_pager_choice(void) {
 	switch (use_pager) {
 	case 0:
@@ -255,19 +211,18 @@ static int handle_alias(int *argcp, const char ***argv)
 	const char **new_argv;
 	const char *alias_command;
 	char *alias_string;
-	int unused_nongit;
-
-	save_env_before_alias();
-	setup_git_directory_gently(&unused_nongit);
 
 	alias_command = (*argv)[0];
 	alias_string = alias_lookup(alias_command);
 	if (alias_string) {
 		if (alias_string[0] == '!') {
 			struct child_process child = CHILD_PROCESS_INIT;
+			int nongit_ok;
+
+			/* Aliases expect GIT_PREFIX, GIT_DIR etc to be set */
+			setup_git_directory_gently(&nongit_ok);
 
 			commit_pager_choice();
-			restore_env(1);
 
 			child.use_shell = 1;
 			argv_array_push(&child.args, alias_string + 1);
@@ -313,8 +268,6 @@ static int handle_alias(int *argcp, const char ***argv)
 		ret = 1;
 	}
 
-	restore_env(0);
-
 	errno = saved_errno;
 
 	return ret;
diff --git a/help.c b/help.c
index f637fc8006..5cdfac7dc2 100644
--- a/help.c
+++ b/help.c
@@ -290,7 +290,7 @@ const char *help_unknown_cmd(const char *cmd)
 	memset(&other_cmds, 0, sizeof(other_cmds));
 	memset(&aliases, 0, sizeof(aliases));
 
-	git_config(git_unknown_cmd_config, NULL);
+	read_early_config(git_unknown_cmd_config, NULL);
 
 	load_command_list("git-", &main_cmds, &other_cmds);
 
diff --git a/setup.c b/setup.c
index 751d02b9be..ae3e0ddda2 100644
--- a/setup.c
+++ b/setup.c
@@ -1004,6 +1004,7 @@ const char *discover_git_directory(struct strbuf *gitdir)
 		warning("ignoring git dir '%s': %s",
 			gitdir->buf + gitdir_offset, err.buf);
 		strbuf_release(&err);
+		strbuf_setlen(gitdir, gitdir_offset);
 		return NULL;
 	}
 
diff --git a/t/t1300-repo-config.sh b/t/t1300-repo-config.sh
index 13b7851f7c..a37ef04222 100755
--- a/t/t1300-repo-config.sh
+++ b/t/t1300-repo-config.sh
@@ -703,6 +703,12 @@ test_expect_success 'invalid unit' '
 	test_i18ngrep "bad numeric config value .1auto. for .aninvalid.unit. in file .git/config: invalid unit" actual
 '
 
+test_expect_success 'line number is reported correctly' '
+	printf "[bool]\n\tvar\n" >invalid &&
+	test_must_fail git config -f invalid --path bool.var 2>actual &&
+	test_i18ngrep "line 2" actual
+'
+
 test_expect_success 'invalid stdin config' '
 	echo "[broken" | test_must_fail git config --list --file - >output 2>&1 &&
 	test_i18ngrep "bad config line 1 in standard input" output
diff --git a/t/t1308-config-set.sh b/t/t1308-config-set.sh
index e495a61616..bafed5c9b8 100755
--- a/t/t1308-config-set.sh
+++ b/t/t1308-config-set.sh
@@ -226,7 +226,9 @@ test_expect_success 'check line errors for malformed values' '
 		br
 	EOF
 	test_expect_code 128 git br 2>result &&
-	test_i18ngrep "fatal: .*alias\.br.*\.git/config.*line 2" result
+	test_i18ngrep "missing value for .alias\.br" result &&
+	test_i18ngrep "fatal: .*\.git/config" result &&
+	test_i18ngrep "fatal: .*line 2" result
 '
 
 test_expect_success 'error on modifying repo config without repo' '
diff --git a/t/t7006-pager.sh b/t/t7006-pager.sh
index 4f3794d415..20b4d83c28 100755
--- a/t/t7006-pager.sh
+++ b/t/t7006-pager.sh
@@ -391,6 +391,17 @@ test_expect_success TTY 'core.pager in repo config works and retains cwd' '
 	)
 '
 
+test_expect_success TTY 'core.pager is found via alias in subdirectory' '
+	sane_unset GIT_PAGER &&
+	test_config core.pager "cat >via-alias" &&
+	(
+		cd sub &&
+		rm -f via-alias &&
+		test_terminal git -c alias.r="-p rev-parse" r HEAD &&
+		test_path_is_file via-alias
+	)
+'
+
 test_doesnt_paginate      expect_failure test_must_fail 'git -p nonsense'
 
 test_pager_choices                       'git shortlog'