fix: Do not use 3way merged checks

When checking for already merged patches, i.e. with `stg push --merged` or
`stg pull --merged`, using 3way patch application creates false-positives
such that StGit would wrongly believe that a patch was already integrated
upstream. This would then lead to the pushed patch becoming empty--which is
bad.

Using non-3way patch application for the already-merged checks solves this
problem.

Author: jpgrayson

src/cmd/refresh.rs

@@ -283,7 +283,7 @@ fn run(matches: &ArgMatches) -> Result<()> {
 
                 if let Some(tree_id) = repo.stupid().with_temp_index(|stupid_temp| {
                     stupid_temp.read_tree(ours)?;
-                    if stupid_temp.apply_treediff_to_index(base, theirs)? {
+                    if stupid_temp.apply_treediff_to_index(base, theirs, true)? {
                         let tree_id = stupid_temp.write_tree()?;
                         Ok(Some(tree_id))
                     } else {

src/cmd/spill.rs

@@ -86,6 +86,7 @@ fn run(matches: &ArgMatches) -> Result<()> {
             stupid_temp.apply_pathlimited_treediff_to_index(
                 patch_commit.tree_id(),
                 parent.tree_id(),
+                true,
                 pathspecs,
             )?;
             stupid_temp.write_tree()

src/cmd/squash.rs

@@ -234,7 +234,7 @@ fn try_squash(
         for commit in patchnames[1..].iter().map(|pn| trans.get_patch_commit(pn)) {
             let parent = commit.parent(0)?;
             if parent.tree_id() != commit.tree_id()
-                && !stupid_temp.apply_treediff_to_index(parent.tree_id(), commit.tree_id())?
+                && !stupid_temp.apply_treediff_to_index(parent.tree_id(), commit.tree_id(), true)?
             {
                 return Ok(None);
             }

src/stack/transaction/mod.rs

@@ -967,7 +967,7 @@ impl<'repo> StackTransaction<'repo> {
                 *temp_index_tree_id = Some(ours);
             }
 
-            let maybe_tree_id = if stupid_temp.apply_treediff_to_index(base, theirs)? {
+            let maybe_tree_id = if stupid_temp.apply_treediff_to_index(base, theirs, true)? {
                 stupid_temp.write_tree().ok()
             } else {
                 None
@@ -1103,9 +1103,11 @@ impl<'repo> StackTransaction<'repo> {
 
             let parent_commit = patch_commit.parent(0)?;
 
-            if stupid_temp
-                .apply_treediff_to_index(patch_commit.tree_id(), parent_commit.tree_id())?
-            {
+            if stupid_temp.apply_treediff_to_index(
+                patch_commit.tree_id(),
+                parent_commit.tree_id(),
+                false,
+            )? {
                 merged.push(patchname);
                 *temp_index_tree_id = None;
             }

src/stupid/mod.rs

@@ -151,6 +151,7 @@ impl<'repo, 'index> StupidContext<'repo, 'index> {
         &self,
         tree1: git2::Oid,
         tree2: git2::Oid,
+        do_3way: bool,
     ) -> Result<bool> {
         if tree1 == tree2 {
             return Ok(true);
@@ -165,9 +166,12 @@ impl<'repo, 'index> StupidContext<'repo, 'index> {
             .stdout(Stdio::piped())
             .spawn_git()?;
 
-        let apply_output = self
-            .git_in_work_root()
-            .args(["apply", "--cached", "--3way"])
+        let mut apply_cmd = self.git_in_work_root();
+        apply_cmd.args(["apply", "--cached"]);
+        if do_3way {
+            apply_cmd.arg("--3way");
+        }
+        let apply_output = apply_cmd
             .stdin(diff_tree_child.stdout.take().unwrap())
             .stdout(Stdio::null())
             .output_git()?
@@ -182,6 +186,7 @@ impl<'repo, 'index> StupidContext<'repo, 'index> {
         &self,
         tree1: git2::Oid,
         tree2: git2::Oid,
+        do_3way: bool,
         pathspecs: SpecIter,
     ) -> Result<bool>
     where
@@ -210,9 +215,12 @@ impl<'repo, 'index> StupidContext<'repo, 'index> {
             return Ok(true);
         }
 
-        let apply_output = self
-            .git_in_work_root()
-            .args(["apply", "--cached", "--3way"])
+        let mut apply_cmd = self.git_in_work_root();
+        apply_cmd.args(["apply", "--cached"]);
+        if do_3way {
+            apply_cmd.arg("--3way");
+        }
+        let apply_output = apply_cmd
             .stdin(Stdio::piped())
             .stdout(Stdio::null())
             .in_and_out(&diff)?;