Merge branch 'stable-6.6' into stable-6.7

* stable-6.6:
  Prepare 6.6.2-SNAPSHOT builds
  JGit v6.6.1.202309021850-r
  Checkout: better directory handling

Change-Id: Ice82d68b2d343a5fac214807cdb369e486481aab

diff --cc org.eclipse.jgit/.settings/.api_filters
index 253ef376869b47ddb7c338a76671471a0f3a7cad,35a3a0aebafeeb677fb43692b3921140eb09fc8d..37dce917837994e3ac812f6be83b4a5deeaf5404
--- 1/org.eclipse.jgit/.settings/.api_filters
--- 2/org.eclipse.jgit/.settings/.api_filters
+++ b/org.eclipse.jgit/.settings/.api_filters
@@@ -1,17 -1,57 +1,33 @@@
  <?xml version="1.0" encoding="UTF-8" standalone="no"?>
  <component id="org.eclipse.jgit" version="2">
 -    <resource path="src/org/eclipse/jgit/errors/PackMismatchException.java" type="org.eclipse.jgit.errors.PackMismatchException">
 -        <filter id="1142947843">
+     <resource path="src/org/eclipse/jgit/dircache/Checkout.java" type="org.eclipse.jgit.dircache.Checkout">
+         <filter id="1109393411">
+             <message_arguments>
+                 <message_argument value="6.6.1"/>
+                 <message_argument value="org.eclipse.jgit.dircache.Checkout"/>
+             </message_arguments>
+         </filter>
+     </resource>
 +    <resource path="src/org/eclipse/jgit/lib/Constants.java" type="org.eclipse.jgit.lib.Constants">
 +        <filter id="388100214">
              <message_arguments>
 -                <message_argument value="5.9.1"/>
 -                <message_argument value="isPermanent()"/>
 +                <message_argument value="org.eclipse.jgit.lib.Constants"/>
 +                <message_argument value="COMMIT_GENERATION_NOT_COMPUTED"/>
              </message_arguments>
          </filter>
 -        <filter id="1142947843">
 +        <filter id="388100214">
              <message_arguments>
 -                <message_argument value="5.9.1"/>
 -                <message_argument value="setPermanent(boolean)"/>
 -            </message_arguments>
 -        </filter>
 -    </resource>
 -    <resource path="src/org/eclipse/jgit/lib/ConfigConstants.java" type="org.eclipse.jgit.lib.ConfigConstants">
 -        <filter id="1142947843">
 -            <message_arguments>
 -                <message_argument value="5.13.2"/>
 -                <message_argument value="CONFIG_KEY_SKIPHASH"/>
 +                <message_argument value="org.eclipse.jgit.lib.Constants"/>
 +                <message_argument value="COMMIT_GENERATION_UNKNOWN"/>
              </message_arguments>
          </filter>
      </resource>
 -    <resource path="src/org/eclipse/jgit/revwalk/RevCommit.java" type="org.eclipse.jgit.revwalk.RevCommit">
 -        <filter id="1193279491">
 -            <message_arguments>
 -                <message_argument value="6.5.1"/>
 -                <message_argument value="buffer"/>
 -            </message_arguments>
 -        </filter>
 -    </resource>
 -    <resource path="src/org/eclipse/jgit/storage/pack/PackConfig.java" type="org.eclipse.jgit.storage.pack.PackConfig">
 -        <filter id="336658481">
 -            <message_arguments>
 -                <message_argument value="org.eclipse.jgit.storage.pack.PackConfig"/>
 -                <message_argument value="DEFAULT_WRITE_REVERSE_INDEX"/>
 -            </message_arguments>
 -        </filter>
 -    </resource>
+     <resource path="src/org/eclipse/jgit/lib/FileModeCache.java" type="org.eclipse.jgit.lib.FileModeCache">
+         <filter id="1109393411">
+             <message_arguments>
+                 <message_argument value="6.6.1"/>
+                 <message_argument value="org.eclipse.jgit.lib.FileModeCache"/>
+             </message_arguments>
+         </filter>
+     </resource>
  </component>

diff --cc org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
Simple merge

diff --cc org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java
Simple merge

diff --cc org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
index 20b27375bd1fc31a5ac65ad0f958c9fe5d83e0e5,d54df8d20e66b9b94c712f9486e37a03c2592f2f..6ae5153c1227d85a9b42b098ea6cc43879b84811
--- 1/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
--- 2/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
@@@ -1521,9 -1479,10 +1507,11 @@@ public class DirCacheCheckout 
         *            {@link WorkingTreeOptions} that are effective; if {@code null}
         *            they are loaded from the repository config
         * @throws java.io.IOException
 +       *             if an IO error occurred
         * @since 6.3
+        * @deprecated since 6.6.1; use {@link Checkout} instead
         */
+       @Deprecated
        public static void checkoutEntry(Repository repo, DirCacheEntry entry,
                        ObjectReader or, boolean deleteRecursive,
                        CheckoutMetadata checkoutMetadata, WorkingTreeOptions options)

diff --cc org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
Simple merge

diff --cc org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
Simple merge

diff --cc org.eclipse.jgit/src/org/eclipse/jgit/patch/PatchApplier.java
Simple merge