fix: Handling of deleted trees on checkout (#2114)

* fix: handling of deleted trees on checkout

* chore: add entry in contributors-rc

* docs: update @gnillev as a contributor

* chore: add unit test

Author: gnillev

js/isomorphic-git/README.md

@@ -389,6 +389,7 @@ Thanks goes to these wonderful people ([emoji key](https://github.com/kentcdodds
     <td align="center"><a href="https://tomlarkworthy.endpointservices.net/"><img src="https://avatars.githubusercontent.com/u/1848162?v=4?s=60" width="60px;" alt=""/><br /><sub><b>Tom Larkworthy</b></sub></a><br /><a href="https://github.com/isomorphic-git/isomorphic-git/commits?author=tomlarkworthy" title="Documentation">📖</a></td>
     <td align="center"><a href="https://github.com/kofta999"><img src="https://avatars.githubusercontent.com/u/99273340?v=4?s=60" width="60px;" alt=""/><br /><sub><b>Mostafa Mahmoud</b></sub></a><br /><a href="https://github.com/isomorphic-git/isomorphic-git/commits?author=kofta999" title="Code">💻</a> <a href="https://github.com/isomorphic-git/isomorphic-git/commits?author=kofta999" title="Tests">⚠️</a> <a href="#question-kofta999" title="Answering Questions">💬</a></td>
     <td align="center"><a href="https://github.com/ARBhosale"><img src="https://avatars.githubusercontent.com/u/26981417?v=4?s=60" width="60px;" alt=""/><br /><sub><b>Aniket Bhosale</b></sub></a><br /><a href="https://github.com/isomorphic-git/isomorphic-git/commits?author=ARBhosale" title="Code">💻</a> <a href="https://github.com/isomorphic-git/isomorphic-git/commits?author=ARBhosale" title="Documentation">📖</a> <a href="https://github.com/isomorphic-git/isomorphic-git/commits?author=ARBhosale" title="Tests">⚠️</a></td>
+    <td align="center"><a href="https://github.com/gnillev"><img src="https://avatars.githubusercontent.com/u/8965094?v=4?s=60" width="60px;" alt=""/><br /><sub><b>Mathias Nisted Velling</b></sub></a><br /><a href="https://github.com/isomorphic-git/isomorphic-git/commits?author=gnillev" title="Code">💻</a><a href="https://github.com/isomorphic-git/isomorphic-git/commits?author=gnillev" title="Tests">⚠️</a></td>
   </tr>
 </table>
 

js/isomorphic-git/index.cjs

@@ -6446,10 +6446,10 @@ async function _checkout({
         if (method === 'rmdir' || method === 'rmdir-index') {
           const filepath = `${dir}/${fullpath}`;
           try {
-            if (method === 'rmdir-index') {
-              index.delete({ filepath: fullpath });
+            if (method === 'rmdir') {
+              await fs.rmdir(filepath);
             }
-            await fs.rmdir(filepath);
+            index.delete({ filepath: fullpath });
             if (onProgress) {
               await onProgress({
                 phase: 'Updating workdir',
@@ -6780,7 +6780,7 @@ async function analyze({
         case '101': {
           switch (await stage.type()) {
             case 'tree': {
-              return ['rmdir', fullpath]
+              return ['rmdir-index', fullpath]
             }
             case 'blob': {
               // Git checks that the workdir.oid === stage.oid before deleting file

js/isomorphic-git/index.js

@@ -6440,10 +6440,10 @@ async function _checkout({
         if (method === 'rmdir' || method === 'rmdir-index') {
           const filepath = `${dir}/${fullpath}`;
           try {
-            if (method === 'rmdir-index') {
-              index.delete({ filepath: fullpath });
+            if (method === 'rmdir') {
+              await fs.rmdir(filepath);
             }
-            await fs.rmdir(filepath);
+            index.delete({ filepath: fullpath });
             if (onProgress) {
               await onProgress({
                 phase: 'Updating workdir',
@@ -6774,7 +6774,7 @@ async function analyze({
         case '101': {
           switch (await stage.type()) {
             case 'tree': {
-              return ['rmdir', fullpath]
+              return ['rmdir-index', fullpath]
             }
             case 'blob': {
               // Git checks that the workdir.oid === stage.oid before deleting file