suggestion: sqldiff add and output file parameter, then it can output all text to a file EXACTLLY.

In windows, use bellow command line can create a diff sql file:

sqldiff.exe --transaction --primarykey src.db target.db > sqldiff.sql

But it has problems when there is a index diff. The diff sql like bellow:

BEGIN TRANSACTION;
CREATE INDEX "col1_binary"

ON "test" (

  "col2" COLLATE BINARY ASC

);
COMMIT;

But after running the diff sql over the src.db, and run the diff command line again, you'll get the diff sql like bellow. Looks like you created the wrong index :

BEGIN TRANSACTION;
DROP INDEX col1_binary;
CREATE INDEX "col1_binary"

ON "test" (

  "col2" COLLATE BINARY ASC

);
COMMIT;

Actually, there extra empty lines:

BEGIN TRANSACTION;
DROP INDEX col1_binary;
CREATE INDEX "col1_binary" [CR]<--
[CRLF]<--
ON "test" ([CR]<--
[CRLF]<--
  "col2" COLLATE BINARY ASC[CR]<--
[CRLF]<--
);[CRLF]<--
COMMIT;

There real patch sql you need is :

BEGIN TRANSACTION;
CREATE INDEX "col1_binary"
ON "test" (
  "col2" COLLATE BINARY ASC
);
COMMIT;

Code changes :

int main(int argc, char **argv){
+  int writeToFile = 0;
  const char *zDb1 = 0;

//-------------------------------------

+    if (strcmp(z, "outputfile") == 0) {
+      if (i == argc - 1) cmdlineError("missing argument to %s", argv[i]);
+        out = fopen(argv[++i], "wb");
+        writeToFile = 1;
+        if (out == 0) cmdlineError("cannot open: %s", argv[i]);
+    }else
    if( strcmp(z,"changeset")==0 ){
    
//-------------------------------------

-  if( useTransaction ) printf("COMMIT;\n");
+  if( useTransaction ) fprintf(out, "COMMIT;\n");
+  if (writeToFile) {
+    fclose(out);
+  }
    

When using the outputfile parameter, the diff sql in the output file is EXACTLY you need!