Fix some “Stage All” special cases (#1037)

* syncIndexWithWorkingDirectory: Fix failure to stage deletions of conflicting files

* syncIndexWithWorkingDirectory: Fix failure to stage unadded submodules

(Not always but) repository folders that weren't registered in .gitmodules would cause the method to fail: “libgit2 error (-4): submodule 'submodules/transfer-photo-albums/' has not been added yet”

* Properly propagate staging errors in -addFilesToIndex:error:

When addFileInWorkingDirectory encountered an error, it would return YES regardless.

* addFilesToIndex: Don't give up after failing to stage a file

Also, rename `shouldWriteRepository` to the more appropriate `needsToWriteIndex`.

* syncIndexWithWorkingDirectory: Fix crash when called with no error pointer

Author: Cykelero

GitUpKit/Extensions/GCRepository+Index.m

@@ -69,24 +69,26 @@ - (BOOL)addFilesToIndex:(NSArray<NSString*>*)paths error:(NSError**)error {
   }
 
   BOOL failed = NO;
-  BOOL shouldWriteRepository = NO;
+  BOOL needsToWriteIndex = NO;
   for (NSString* path in paths) {
     if (![self addFileInWorkingDirectory:path toIndex:index error:error] || (error && *error != nil)) {
       failed = YES;
-      break;
+      continue;
     }
 
-    shouldWriteRepository = YES;
+    needsToWriteIndex = YES;
   }
 
-  if (failed && shouldWriteRepository) {
-    if (shouldWriteRepository) {
+  if (needsToWriteIndex) {
+    if (failed) {
       [self writeRepositoryIndex:index error:NULL];
+      return NO;
     }
-    return NO;
+
+    return [self writeRepositoryIndex:index error:error];
   }
 
-  return [self writeRepositoryIndex:index error:error];
+  return !failed;
 }
 
 - (BOOL)resetFileInIndexToHEAD:(NSString*)path error:(NSError**)error {

GitUpKit/Extensions/GCRepository+Utilities.m

@@ -205,11 +205,21 @@ - (BOOL)syncIndexWithWorkingDirectory:(NSError**)error {
         if (delta.submodule) {
           GCSubmodule* submodule = [self lookupSubmoduleWithName:delta.canonicalPath error:error];
           if (!submodule || ![self addSubmoduleToRepositoryIndex:submodule error:error]) {
-            return NO;
+            BOOL wasJustTryingToStageAnUntrackedSubmodule = error && [[*error localizedDescription] hasSuffix:@"' has not been added yet"];
+            
+            if (!wasJustTryingToStageAnUntrackedSubmodule) {
+              return NO;
+            }
           }
         } else {
           if (![self addFileInWorkingDirectory:delta.canonicalPath toIndex:index error:error]) {
-            return NO;
+            BOOL wasJustTryingToStageADeletedConflictingFile =
+              delta.change == kGCFileDiffChange_Conflicted
+              && (error && [[*error localizedDescription] isEqualToString:@"No such file or directory"]);
+            
+            if (!wasJustTryingToStageADeletedConflictingFile) {
+              return NO;
+            }
           }
         }
         break;