This patch fixes a bug where outdated files cannot be updated.
See the regression test added in this patch for a reproduction recipe.
(I think semarie saw a similar issue recently; Perhaps it was this bug?)

The problem happens after 'got update' skips a conflicted file,
which looks like this:

  $ got update
  #  beta
  Updated to commit abcde12345...
  Files not updated because of existing merge conflicts: 1
 
When this occurs, the file index entry for 'beta' should remain unchanged.
However, the base commit ID for this entry is bumped along with any other
updated entries. This is wrong since the file was not actually updated.
The file index is now slightly corrupt: The base blob recorded for 'beta'
doesn't actually exist in the base commit recorded for 'beta', and the
recorded base commit is incorrect.

A subsequent 'got update' will see the incorrect base commit ID on
beta's entry and consider the file as already up-to-date.

We can fix this issue by simply leaving the entry's base commit ID as-is.

ok?

diff 867b03e66abeaeadc44ef9978e89d71504e15cba 784f2e14750a58132ab6e650e20d483ab120cc48
blob - d1e3839c06a7f70e71410592024f426053df2ced
blob + aec06af5925a0cd63ffc6b150466bad036d5abd8
--- lib/fileindex.c
+++ lib/fileindex.c
@@ -46,6 +46,7 @@
 #define GOT_FILEIDX_F_NO_COMMIT		0x00040000
 #define GOT_FILEIDX_F_NO_FILE_ON_DISK	0x00080000
 #define GOT_FILEIDX_F_REMOVE_ON_FLUSH	0x00100000
+#define GOT_FILEIDX_F_SKIPPED		0x00200000
 
 struct got_fileindex {
 	struct got_fileindex_tree entries;
@@ -146,6 +147,12 @@ got_fileindex_entry_mark_deleted_from_disk(struct got_
 	ie->flags |= GOT_FILEIDX_F_NO_FILE_ON_DISK;
 }
 
+void
+got_fileindex_entry_mark_skipped(struct got_fileindex_entry *ie)
+{
+	ie->flags |= GOT_FILEIDX_F_SKIPPED;
+}
+
 const struct got_error *
 got_fileindex_entry_alloc(struct got_fileindex_entry **ie,
     const char *relpath)
@@ -245,6 +252,12 @@ got_fileindex_entry_has_file_on_disk(struct got_filein
 	return (ie->flags & GOT_FILEIDX_F_NO_FILE_ON_DISK) == 0;
 }
 
+int
+got_fileindex_entry_was_skipped(struct got_fileindex_entry *ie)
+{
+	return (ie->flags & GOT_FILEIDX_F_SKIPPED) != 0;
+}
+
 static const struct got_error *
 add_entry(struct got_fileindex *fileindex, struct got_fileindex_entry *ie)
 {
@@ -497,6 +510,7 @@ got_fileindex_write(struct got_fileindex *fileindex, F
 
 	RB_FOREACH_SAFE(ie, got_fileindex_tree, &fileindex->entries, tmp) {
 		ie->flags &= ~GOT_FILEIDX_F_NOT_FLUSHED;
+		ie->flags &= ~GOT_FILEIDX_F_SKIPPED;
 		if (ie->flags & GOT_FILEIDX_F_REMOVE_ON_FLUSH) {
 			RB_REMOVE(got_fileindex_tree, &fileindex->entries, ie);
 			got_fileindex_entry_free(ie);
blob - 537374d719e84293f1b449465ab63e092b44a20a
blob + d03058e83c5f5c0a69baf66795455eb3ab8b7af7
--- lib/got_lib_fileindex.h
+++ lib/got_lib_fileindex.h
@@ -109,6 +109,7 @@ mode_t got_fileindex_perms_to_st(struct got_fileindex_
 
 const struct got_error *got_fileindex_entry_update(struct got_fileindex_entry *,
     int, const char *, uint8_t *, uint8_t *, int);
+void got_fileindex_entry_mark_skipped(struct got_fileindex_entry *);
 const struct got_error *got_fileindex_entry_alloc(struct got_fileindex_entry **,
     const char *);
 void got_fileindex_entry_free(struct got_fileindex_entry *);
@@ -164,6 +165,7 @@ const struct got_error *got_fileindex_diff_dir(struct 
 int got_fileindex_entry_has_blob(struct got_fileindex_entry *);
 int got_fileindex_entry_has_commit(struct got_fileindex_entry *);
 int got_fileindex_entry_has_file_on_disk(struct got_fileindex_entry *);
+int got_fileindex_entry_was_skipped(struct got_fileindex_entry *);
 uint32_t got_fileindex_entry_stage_get(const struct got_fileindex_entry *);
 void got_fileindex_entry_stage_set(struct got_fileindex_entry *ie, uint32_t);
 int got_fileindex_entry_filetype_get(struct got_fileindex_entry *);
blob - c6a9ee611f39f7106cbf6b33215f75f9f7a5c715
blob + 385e8a46c03c7be4c81ce76af599d43f216ed948
--- lib/worktree.c
+++ lib/worktree.c
@@ -1951,6 +1951,8 @@ update_blob(struct got_worktree *worktree,
 		goto done;
 	}
 	if (status == GOT_STATUS_CONFLICT) {
+		if (ie)
+			got_fileindex_entry_mark_skipped(ie);
 		err = (*progress_cb)(progress_arg, GOT_STATUS_CANNOT_UPDATE,
 		    path);
 		goto done;
@@ -2474,6 +2476,9 @@ bump_base_commit_id(void *arg, struct got_fileindex_en
 	} else if (!got_path_is_child(ie->path, a->path, a->path_len))
 		return NULL;
 
+	if (got_fileindex_entry_was_skipped(ie))
+		return NULL;
+
 	if (memcmp(ie->commit_sha1, a->base_commit_id->sha1,
 	    SHA1_DIGEST_LENGTH) == 0)
 		return NULL;
blob - fa0398814a0312e4d8d4d343c490f6b7b4129804
blob + 18691664018f8a6afd325e890af93afbcdd51b2b
--- regress/cmdline/update.sh
+++ regress/cmdline/update.sh
@@ -2391,7 +2391,188 @@ test_update_single_file() {
 	return 0
 }
 
+test_update_file_skipped_due_to_conflict() {
+	local testroot=`test_init update_file_skipped_due_to_conflict`
+	local commit_id0=`git_show_head $testroot/repo`
+	blob_id0=`get_blob_id $testroot/repo "" beta`
 
+	echo "changed beta" > $testroot/repo/beta
+	git_commit $testroot/repo -m "changed beta"
+	local commit_id1=`git_show_head $testroot/repo`
+	blob_id1=`get_blob_id $testroot/repo "" beta`
+
+	got checkout $testroot/repo $testroot/wt > /dev/null
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	blob_id=`(cd $testroot/wt && got info beta | grep 'blob:' | \
+		cut -d ':' -f 2 | tr -d ' ')`
+	if [ "$blob_id" != "$blob_id1" ]; then
+		echo "file beta has the wrong base blob ID" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+
+	commit_id=`(cd $testroot/wt && got info beta | \
+		grep 'based on commit:' | cut -d ':' -f 2 | tr -d ' ')`
+	if [ "$commit_id" != "$commit_id1" ]; then
+		echo "file beta has the wrong base commit ID" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+
+	echo "modified beta" > $testroot/wt/beta
+
+	(cd $testroot/wt && got update -c $commit_id0 > $testroot/stdout)
+
+	echo "C  beta" > $testroot/stdout.expected
+	echo "Updated to commit $commit_id0" >> $testroot/stdout.expected
+	echo "Files with new merge conflicts: 1" >> $testroot/stdout.expected
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	echo "<<<<<<< merged change: commit $commit_id0" \
+		> $testroot/content.expected
+	echo "beta" >> $testroot/content.expected
+	echo "||||||| 3-way merge base: commit $commit_id1" \
+		>> $testroot/content.expected
+	echo "changed beta" >> $testroot/content.expected
+	echo "=======" >> $testroot/content.expected
+	echo "modified beta" >> $testroot/content.expected
+	echo ">>>>>>>" >> $testroot/content.expected
+
+	cat $testroot/wt/beta > $testroot/content
+
+	cmp -s $testroot/content.expected $testroot/content
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/content.expected $testroot/content
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	blob_id=`(cd $testroot/wt && got info beta | grep 'blob:' | \
+		cut -d ':' -f 2 | tr -d ' ')`
+	if [ "$blob_id" != "$blob_id0" ]; then
+		echo "file beta has the wrong base blob ID" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+
+	commit_id=`(cd $testroot/wt && got info beta | \
+		grep 'based on commit:' | cut -d ':' -f 2 | tr -d ' ')`
+	if [ "$commit_id" != "$commit_id0" ]; then
+		echo "file beta has the wrong base commit ID" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+
+	# update to the latest commit again; this skips beta
+	(cd $testroot/wt && got update > $testroot/stdout)
+	echo "#  beta" > $testroot/stdout.expected
+	echo "Updated to commit $commit_id1" >> $testroot/stdout.expected
+	echo "Files not updated because of existing merge conflicts: 1" \
+		>> $testroot/stdout.expected
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	# blob ID of beta should not have changed
+	blob_id=`(cd $testroot/wt && got info beta | grep 'blob:' | \
+		cut -d ':' -f 2 | tr -d ' ')`
+	if [ "$blob_id" != "$blob_id0" ]; then
+		echo "file beta has the wrong base blob ID" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+
+	# commit ID of beta should not have changed; There was a bug
+	# here where the commit ID had been changed even though the
+	# file was not updated.
+	commit_id=`(cd $testroot/wt && got info beta | \
+		grep 'based on commit:' | cut -d ':' -f 2 | tr -d ' ')`
+	if [ "$commit_id" != "$commit_id0" ]; then
+		echo "file beta has the wrong base commit ID: $commit_id" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+
+	# beta is still conflicted and based on commit 0
+	echo 'C  beta' > $testroot/stdout.expected
+	(cd $testroot/wt && got status > $testroot/stdout)
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	# resolve the conflict via revert
+	(cd $testroot/wt && got revert beta >/dev/null)
+
+	# beta now matches its base blob which is still from commit 0
+	echo "beta" > $testroot/content.expected
+	cat $testroot/wt/beta > $testroot/content
+	cmp -s $testroot/content.expected $testroot/content
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/content.expected $testroot/content
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	# updating to the latest commit should now update beta
+	(cd $testroot/wt && got update > $testroot/stdout)
+	echo "U  beta" > $testroot/stdout.expected
+	echo "Updated to commit $commit_id1" >> $testroot/stdout.expected
+	cmp -s $testroot/stdout.expected $testroot/stdout
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/stdout.expected $testroot/stdout
+		test_done "$testroot" "$ret"
+		return 1
+	fi
+
+	blob_id=`(cd $testroot/wt && got info beta | grep 'blob:' | \
+		cut -d ':' -f 2 | tr -d ' ')`
+	if [ "$blob_id" != "$blob_id1" ]; then
+		echo "file beta has the wrong base blob ID" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+
+	commit_id=`(cd $testroot/wt && got info beta | \
+		grep 'based on commit:' | cut -d ':' -f 2 | tr -d ' ')`
+	if [ "$commit_id" != "$commit_id1" ]; then
+		echo "file beta has the wrong base commit ID: $commit_id" >&2
+		test_done "$testroot" "1"
+		return 1
+	fi
+
+	echo "changed beta" > $testroot/content.expected
+	cat $testroot/wt/beta > $testroot/content
+	cmp -s $testroot/content.expected $testroot/content
+	ret="$?"
+	if [ "$ret" != "0" ]; then
+		diff -u $testroot/content.expected $testroot/content
+	fi
+	test_done "$testroot" "$ret"
+}
+
+
 test_parseargs "$@"
 run_test test_update_basic
 run_test test_update_adds_file
@@ -2432,3 +2613,4 @@ run_test test_update_adds_symlink
 run_test test_update_deletes_symlink
 run_test test_update_symlink_conflicts
 run_test test_update_single_file
+run_test test_update_file_skipped_due_to_conflict