Fix issue #2842: Handle qpdf exit code 3 as success with warnings (#2883)

# Description of Changes

Please provide a summary of the changes, including:

- **What was changed**:
- Modified the `ProcessExecutor` class to accept exit code `3` from
**qpdf** as a success with warnings.
- Added a check to ensure that only **qpdf**’s exit code `3` is treated
as a warning.
- Added a warning log for **qpdf** exit code `3` to provide better
visibility into the repair process.

- **Why the change was made**:
- The repair process was failing when **qpdf** returned exit code `3`,
even though the operation succeeded with warnings. This caused
unnecessary errors for users.
- The changes ensure that PDFs with minor structural issues (e.g.,
mismatched object counts) are still repaired successfully, while logging
warnings for transparency.
- Added a check to ensure that only **qpdf**’s exit code `3` is treated
as a warning, preventing potential issues with other tools that might
use exit code `3` for actual errors.

Closes #2842

---

## Checklist

### General

- [x] I have read the [Contribution
Guidelines](https://github.com/Stirling-Tools/Stirling-PDF/blob/main/CONTRIBUTING.md)
- [x] I have read the [Stirling-PDF Developer
Guide](https://github.com/Stirling-Tools/Stirling-PDF/blob/main/DeveloperGuide.md)
(if applicable)
- [x] I have performed a self-review of my own code
- [x] My changes generate no new warnings

### Testing (if applicable)

- [x] I have tested my changes locally.
- Verified that exit code `3` is only treated as a warning for **qpdf**
and not for other tools.

---

### Additional Notes
- The changes align with **qpdf**'s behavior, where exit code `3`
indicates a successful operation with warnings.
- Added a check to ensure that only **qpdf**’s exit code `3` is treated
as a warning, preventing potential issues with other tools.

Co-authored-by: Anthony Stirling <77850077+Frooodle@users.noreply.github.com>

src/main/java/stirling/software/SPDF/utils/ProcessExecutor.java

@@ -218,6 +218,9 @@ public class ProcessExecutor {
             errorReaderThread.join();
             outputReaderThread.join();
 
+            boolean isQpdf =
+                    command != null && !command.isEmpty() && command.get(0).contains("qpdf");
+
             if (outputLines.size() > 0) {
                 String outputMessage = String.join("\n", outputLines);
                 messages += outputMessage;
@@ -233,6 +236,9 @@ public class ProcessExecutor {
                     log.warn("Command error output:\n" + errorMessage);
                 }
                 if (exitCode != 0) {
+                    if (isQpdf && exitCode == 3) {
+                        log.warn("qpdf succeeded with warnings: {}", messages);
+                    } else {
                         throw new IOException(
                                 "Command process failed with exit code "
                                         + exitCode
@@ -240,14 +246,19 @@ public class ProcessExecutor {
                                         + errorMessage);
                     }
                 }
+            }
 
             if (exitCode != 0) {
+                if (isQpdf && exitCode == 3) {
+                    log.warn("qpdf succeeded with warnings: {}", messages);
+                } else {
                     throw new IOException(
                             "Command process failed with exit code "
                                     + exitCode
                                     + "\nLogs: "
                                     + messages);
                 }
+            }
         } finally {
             semaphore.release();
         }