From 42462a32582d19733fad3ea41c274084ac7da1a7 Mon Sep 17 00:00:00 2001
From: ghidragon <106987263+ghidragon@users.noreply.github.com>
Date: Wed, 18 Sep 2024 13:38:38 -0400
Subject: [PATCH] GP-4921 fixed change markers after a check-in with the
 program open in the tool

---
 .../misc/MyProgramChangesDisplayPlugin.java   |  6 +--
 .../database/ProgramContentHandler.java       | 18 +++++----
 .../program/database/ProgramDBChangeSet.java  | 37 +++++++++++--------
 3 files changed, 34 insertions(+), 27 deletions(-)

diff --git a/Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/misc/MyProgramChangesDisplayPlugin.java b/Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/misc/MyProgramChangesDisplayPlugin.java
index 0ae89ed0fc..4ae8aca1ab 100644
--- a/Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/misc/MyProgramChangesDisplayPlugin.java
+++ b/Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/misc/MyProgramChangesDisplayPlugin.java
@@ -4,9 +4,9 @@
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  *      http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -279,7 +279,7 @@ public class MyProgramChangesDisplayPlugin extends ProgramPlugin implements Doma
 		}
 
 		if (isTrackingServerChanges()) {
-			if (programSaved) {
+			if (programSaved || programChangedRemotely) {
 				currentChangesSinceCheckoutMarks
 						.setAddressSetCollection(changeSet.getAddressSetCollectionSinceCheckout());
 			}
diff --git a/Ghidra/Framework/SoftwareModeling/src/main/java/ghidra/program/database/ProgramContentHandler.java b/Ghidra/Framework/SoftwareModeling/src/main/java/ghidra/program/database/ProgramContentHandler.java
index 808f1342d4..d5ee0f23e4 100644
--- a/Ghidra/Framework/SoftwareModeling/src/main/java/ghidra/program/database/ProgramContentHandler.java
+++ b/Ghidra/Framework/SoftwareModeling/src/main/java/ghidra/program/database/ProgramContentHandler.java
@@ -4,9 +4,9 @@
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  *      http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -78,7 +78,7 @@ public class ProgramContentHandler extends DBWithUserDataContentHandler<ProgramD
 			bf = dbItem.open(version, minChangeVersion);
 			dbh = new DBHandle(bf);
 			program = new ProgramDB(dbh, OpenMode.IMMUTABLE, monitor, consumer);
-			getProgramChangeSet(program, bf);
+			loadProgramChangeSet(program, bf);
 			success = true;
 			return program;
 		}
@@ -130,7 +130,7 @@ public class ProgramContentHandler extends DBWithUserDataContentHandler<ProgramD
 			dbh = new DBHandle(bf);
 			OpenMode openMode = okToUpgrade ? OpenMode.UPGRADE : OpenMode.UPDATE;
 			program = new ProgramDB(dbh, openMode, monitor, consumer);
-			getProgramChangeSet(program, bf);
+			loadProgramChangeSet(program, bf);
 			program.setProgramUserData(new ProgramUserDataDB(program));
 			success = true;
 			return program;
@@ -184,7 +184,7 @@ public class ProgramContentHandler extends DBWithUserDataContentHandler<ProgramD
 			OpenMode openMode = okToUpgrade ? OpenMode.UPGRADE : OpenMode.UPDATE;
 			program = new ProgramDB(dbh, openMode, monitor, consumer);
 			if (checkoutId == FolderItem.DEFAULT_CHECKOUT_ID) {
-				getProgramChangeSet(program, bf);
+				loadProgramChangeSet(program, bf);
 			}
 			if (recover) {
 				recoverChangeSet(program, dbh);
@@ -255,9 +255,11 @@ public class ProgramContentHandler extends DBWithUserDataContentHandler<ProgramD
 		}
 	}
 
-	private ProgramDBChangeSet getProgramChangeSet(ProgramDB program, ManagedBufferFile bf)
+	private ProgramDBChangeSet loadProgramChangeSet(ProgramDB program, ManagedBufferFile bf)
 			throws IOException {
 		ProgramDBChangeSet changeSet = (ProgramDBChangeSet) program.getChangeSet();
+		changeSet.clearAll();
+
 		BufferFile cf = bf.getNextChangeDataFile(true);
 		DBHandle cfh = null;
 		while (cf != null) {
@@ -292,7 +294,7 @@ public class ProgramContentHandler extends DBWithUserDataContentHandler<ProgramD
 			bf = dbItem.open(toVer, fromVer);
 			dbh = new DBHandle(bf);
 			program = new ProgramDB(dbh, OpenMode.IMMUTABLE, null, this);
-			return getProgramChangeSet(program, bf);
+			return loadProgramChangeSet(program, bf);
 		}
 		catch (VersionException | IOException e) {
 			throw e;
@@ -374,7 +376,7 @@ public class ProgramContentHandler extends DBWithUserDataContentHandler<ProgramD
 		}
 		LocalManagedBufferFile bf = dbItem.openForUpdate(FolderItem.DEFAULT_CHECKOUT_ID);
 		program.getDBHandle().setDBVersionedSourceFile(bf);
-		getProgramChangeSet(program, bf);
+		loadProgramChangeSet(program, bf);
 	}
 
 }
diff --git a/Ghidra/Framework/SoftwareModeling/src/main/java/ghidra/program/database/ProgramDBChangeSet.java b/Ghidra/Framework/SoftwareModeling/src/main/java/ghidra/program/database/ProgramDBChangeSet.java
index ab8f7ffdaf..857ca14c4a 100644
--- a/Ghidra/Framework/SoftwareModeling/src/main/java/ghidra/program/database/ProgramDBChangeSet.java
+++ b/Ghidra/Framework/SoftwareModeling/src/main/java/ghidra/program/database/ProgramDBChangeSet.java
@@ -4,9 +4,9 @@
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * 
+ *
  *      http://www.apache.org/licenses/LICENSE-2.0
- * 
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -361,25 +361,29 @@ class ProgramDBChangeSet implements ProgramChangeSet, DomainObjectDBChangeSet {
 		}
 
 		if (!isCheckedOut) { // if not versioned, wipe out change sets
-			changedAddrsSinceCheckout.clear();
-			changedRegAddrsSinceCheckout.clear();
-			changedAddrsSinceSave.clear();
-			changedRegAddrsSinceSave.clear();
-			changedCategoryIds.clear();
-			changedDataTypeIds.clear();
-			changedProgramTreeIds.clear();
-			changedSymbolIds.clear();
-			changedSourceArchiveIds.clear();
-			addedCategoryIds.clear();
-			addedDataTypeIds.clear();
-			addedProgramTreeIds.clear();
-			addedSymbolIds.clear();
-			addedSourceArchiveIds.clear();
+			clearAll();
 		}
 
 		clearUndo();
 	}
 
+	void clearAll() {
+		changedAddrsSinceCheckout.clear();
+		changedRegAddrsSinceCheckout.clear();
+		changedAddrsSinceSave.clear();
+		changedRegAddrsSinceSave.clear();
+		changedCategoryIds.clear();
+		changedDataTypeIds.clear();
+		changedProgramTreeIds.clear();
+		changedSymbolIds.clear();
+		changedSourceArchiveIds.clear();
+		addedCategoryIds.clear();
+		addedDataTypeIds.clear();
+		addedProgramTreeIds.clear();
+		addedSymbolIds.clear();
+		addedSourceArchiveIds.clear();
+	}
+
 	@Override
 	public synchronized void startTransaction() {
 		inTransaction = true;
@@ -659,6 +663,7 @@ class ProgramDBChangeSet implements ProgramChangeSet, DomainObjectDBChangeSet {
 		}
 		return true;
 	}
+
 }
 
 class ChangeDiff {