just-mr: Fix handling of .gitignore files in git repositories

The command 'git add .' does not include paths found in .gitignore
files in the directory tree where the command is issued. This is
not the desired behaviour, as we expect for a tree with a given
commit id to contain all of the entries, irrespective of their
meaning to Git.

This commit addresses the issue as described.

For the just-mr.py script we modified the staging command to
'git add -f .'.

For the compiled just-mr, simply adding the force flag to
'git_index_add_all' did not work as intended for files found in
ignored subdirectories. This is a known libgit2 issue which has
been fixed in v1.6.3. Until we can upgrade our libgit2 version,
a workaround was implemented: we recursively read the directory
entries ourselves and add each of them iteratively using
'git_index_add_bypath', making sure to ignore the root '.git'
subtree (which cannot be staged).

At the moment the handling of Git submodules remains an open issue,
as Git does not allow '.git' subtrees to be forcefully added to the
index, and thus such directory entries will currently not be
considered as part of a git tree. This however is consistent
behavior between Git and libgit2.

(cherry picked from f234434a6fa2118b10765cff2f75bbc3196fec39)

1 files changed, 30 insertions, 12 deletions

diff --git a/src/buildtool/file_system/git_repo.cpp b/src/buildtool/file_system/git_repo.cpp
index 9fe63fb6..2df31960 100644
--- a/src/buildtool/file_system/git_repo.cpp
+++ b/src/buildtool/file_system/git_repo.cpp
@@ -16,6 +16,7 @@
 
 #include <thread>
 
+#include "src/buildtool/file_system/file_system_manager.hpp"
 #include "src/buildtool/logging/logger.hpp"
 #include "src/utils/cpp/gsl.hpp"
 #include "src/utils/cpp/hex_string.hpp"
@@ -353,9 +354,15 @@ GitRepo::GitRepo(std::filesystem::path const& repo_path) noexcept {
         }
         cas->odb_.reset(odb_ptr);  // retain odb pointer
         is_repo_fake_ = false;
-        // save root path
-        cas->git_path_ = ToNormalPath(std::filesystem::absolute(
-            std::filesystem::path(git_repository_path(repo_->Ptr()))));
+        // save root path; this differs if repository is bare or not
+        if (git_repository_is_bare(repo_->Ptr()) != 0) {
+            cas->git_path_ = std::filesystem::absolute(
+                ToNormalPath(git_repository_path(repo_->Ptr())));
+        }
+        else {
+            cas->git_path_ = std::filesystem::absolute(
+                ToNormalPath(git_repository_workdir(repo_->Ptr())));
+        }
         // retain the pointer
         git_cas_ = std::static_pointer_cast<GitCAS const>(cas);
     } catch (std::exception const& ex) {
@@ -477,19 +484,32 @@ auto GitRepo::StageAndCommitAllAnonymous(std::string const& message,
         // share the odb lock
         std::shared_lock lock{GetGitCAS()->mutex_};
 
+        // cannot perform this operation on a bare repository; this has to be
+        // checked because git_index_add_bypath will not do it for us!
+        if (not FileSystemManager::Exists(GetGitCAS()->git_path_ / ".git")) {
+            (*logger)("cannot stage and commit files in a bare repository!",
+                      true /*fatal*/);
+            return std::nullopt;
+        }
+
         // add all files to be staged
         git_index* index_ptr{nullptr};
         git_repository_index(&index_ptr, repo_->Ptr());
         auto index = std::unique_ptr<git_index, decltype(&index_closer)>(
             index_ptr, index_closer);
 
-        git_strarray array_obj{};
-        PopulateStrarray(&array_obj, {"."});
-        auto array = std::unique_ptr<git_strarray, decltype(&strarray_deleter)>(
-            &array_obj, strarray_deleter);
-
-        if (git_index_add_all(index.get(), array.get(), 0, nullptr, nullptr) !=
-            0) {
+        // due to mismanagement of .gitignore rules by libgit2 when doing a
+        // forced add all, we resort to using git_index_add_bypath manually for
+        // all entries, instead of git_index_add_all with GIT_INDEX_ADD_FORCE.
+        auto use_entry = [&index](std::filesystem::path const& name,
+                                  bool is_tree) {
+            return is_tree or
+                   git_index_add_bypath(index.get(), name.c_str()) == 0;
+        };
+        if (not FileSystemManager::ReadDirectoryEntriesRecursive(
+                GetGitCAS()->git_path_,
+                use_entry,
+                /*ignored_subdirs=*/{".git"})) {
             (*logger)(fmt::format(
                           "staging files in git repository {} failed with:\n{}",
                           GetGitCAS()->git_path_.string(),
@@ -497,8 +517,6 @@ auto GitRepo::StageAndCommitAllAnonymous(std::string const& message,
                       true /*fatal*/);
             return std::nullopt;
         }
-        // release unused resources
-        array.reset(nullptr);
         // build tree from staged files
         git_oid tree_oid;
         if (git_index_write_tree(&tree_oid, index.get()) != 0) {