Eliminate all remaining uses of git2::Index

This relates to sparse checkout support (#195). git2 does not comprehend
sparse checkouts and thus using any index <=> worktree operations is likely
to break sparse checkouts. Most important index operations have already
been converted to using git commands, this gets all the remaining
instances.

N.B. in run_pre_commit_hook(), GIT_INDEX_FILE is no longer being supplied
explicitly. In all of StGit's use cases either using the default index or
inheriting GIT_INDEX_FILE from the calling environment should be okay.

Author: jpgrayson

src/cmd/clean.rs

@@ -11,6 +11,7 @@ use crate::{
     patchname::PatchName,
     repo::RepositoryExtended,
     stack::{Stack, StackStateAccess},
+    stupid::Stupid,
 };
 
 use super::StGitCommand;
@@ -72,7 +73,7 @@ fn run(matches: &ArgMatches) -> Result<()> {
                     // Do not clean the topmost patch if there are outstanding
                     // conflicts. The patch is only empty because the conflicts caused
                     // its contents to be dumped into the index and worktree.
-                    if !repo.index()?.has_conflicts() {
+                    if repo.stupid().statuses(None)?.check_conflicts().is_ok() {
                         to_delete.push(pn.clone());
                     }
                 } else {

src/cmd/spill.rs

@@ -82,7 +82,6 @@ fn run(matches: &ArgMatches) -> Result<()> {
         .clone();
     let patch_commit = stack.get_patch_commit(&patchname);
     let parent = patch_commit.parent(0)?;
-    let mut index = repo.index()?;
 
     let tree_id = if let Some(pathspecs) = matches.get_many::<PathBuf>("pathspecs") {
         stupid.with_temp_index(|stupid_temp| {
@@ -120,9 +119,7 @@ fn run(matches: &ArgMatches) -> Result<()> {
         .execute(&reflog_msg)?;
 
     if matches.contains_id("reset") {
-        let tree = repo.find_tree(tree_id)?;
-        index.read_tree(&tree)?;
-        index.write()?;
+        stupid.read_tree(tree_id)?;
     }
 
     Ok(())

src/cmd/sync.rs

@@ -303,11 +303,8 @@ fn series_merge_patch(
         }
     }
 
-    let mut index = trans.repo().index()?;
-    index.read(true)?;
-    index.update_all(changed_paths, None)?;
-    index.write()?;
-    let tree_id = index.write_tree()?;
+    stupid.update_index(Some(changed_paths))?;
+    let tree_id = stupid.write_tree()?;
 
     stupid.read_tree_checkout(tree_id, trans.stack().branch_head.tree_id())?;
     if !stupid.merge_recursive(

src/hook.rs

@@ -54,16 +54,13 @@ pub(crate) fn run_pre_commit_hook(repo: &git2::Repository, use_editor: bool) ->
     let workdir = repo
         .workdir()
         .expect("should not get this far with a bare repo");
-    hook_command.current_dir(workdir);
     if !use_editor {
         hook_command.env("GIT_EDITOR", ":");
     }
-    let index = repo.index().expect("gotta have an index");
-    let index_path = index.path().expect("index must be a file");
-    hook_command.env("GIT_INDEX_FILE", index_path);
-    hook_command.stdin(std::process::Stdio::null());
 
     let status = hook_command
+        .current_dir(workdir)
+        .stdin(std::process::Stdio::null())
         .status()
         .with_context(|| format!("`{hook_name}` hook"))?;