Improved Configuration and YAML Management (#2966)

# Description of Changes

**What was changed:**
- **Configuration Updates:**  
Replaced all calls to `GeneralUtils.saveKeyToConfig` with the new
`GeneralUtils.saveKeyToSettings` method across multiple classes (e.g.,
`LicenseKeyChecker`, `InitialSetup`, `SettingsController`, etc.). This
update ensures consistent management of configuration settings.
  
- **File Path and Exception Handling:**  
Updated file path handling in `SPDFApplication` by creating `Path`
objects from string paths and logging these paths for clarity. Also
refined exception handling by catching more specific exceptions (e.g.,
using `IOException` instead of a generic `Exception`).

- **Analytics Flag and Rate Limiting:**  
Changed the analytics flag in the application properties from a `String`
to a `Boolean`, and updated related logic in `AppConfig` and
`PostHogService`. The rate-limiting property retrieval in `AppConfig`
was also refined for clarity.

- **YAML Configuration Management:**  
Replaced the previous manual, line-based YAML merging logic in
`ConfigInitializer` with a new `YamlHelper` class. This helper leverages
the SnakeYAML engine to load, update, and save YAML configurations more
robustly while preserving comments and formatting.

**Why the change was made:**
- **Improved Maintainability:**  
Consolidating configuration update logic into a single utility method
(`saveKeyToSettings`) reduces code duplication and simplifies future
maintenance.
  
- **Enhanced Robustness:**  
The new `YamlHelper` class ensures that configuration files are merged
accurately and safely, minimizing risks of data loss or format
corruption.
  
- **Better Type Safety and Exception Handling:**  
Switching the analytics flag to a Boolean and refining exception
handling improves code robustness and debugging efficiency.
  
- **Clarity and Consistency:**  
Standardizing file path handling and logging practices enhances code
readability across the project.

**Challenges encountered:**
- **YAML Merging Complexity:**  
Integrating the new `YamlHelper` required careful handling to preserve
existing settings, comments, and formatting during merges.
  
- **Type Conversion and Backward Compatibility:**  
Updating the analytics flag from a string to a Boolean required
extensive testing to ensure backward compatibility and proper
functionality.
  
- **Exception Granularity:**  
Refactoring exception handling from a generic to a more specific
approach involved a detailed review to cover all edge cases.

Closes #<issue_number>

---

## Checklist

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

### Documentation

- [ ] I have updated relevant docs on [Stirling-PDF's doc
repo](https://github.com/Stirling-Tools/Stirling-Tools.github.io/blob/main/docs/)
(if functionality has heavily changed)
- [ ] I have read the section [Add New Translation
Tags](https://github.com/Stirling-Tools/Stirling-PDF/blob/main/HowToAddNewLanguage.md#add-new-translation-tags)
(for new translation tags only)

### UI Changes (if applicable)

- [ ] Screenshots or videos demonstrating the UI changes are attached
(e.g., as comments or direct attachments in the PR)

### Testing (if applicable)

- [x] I have tested my changes locally. Refer to the [Testing
Guide](https://github.com/Stirling-Tools/Stirling-PDF/blob/main/DeveloperGuide.md#6-testing)
for more details.

---------

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

src/main/java/stirling/software/SPDF/config/InitialSetup.java

@@ -44,7 +44,7 @@ public class InitialSetup {
         if (!GeneralUtils.isValidUUID(uuid)) {
             // Generating a random UUID as the secret key
             uuid = UUID.randomUUID().toString();
-            GeneralUtils.saveKeyToConfig("AutomaticallyGenerated.UUID", uuid);
+            GeneralUtils.saveKeyToSettings("AutomaticallyGenerated.UUID", uuid);
             applicationProperties.getAutomaticallyGenerated().setUUID(uuid);
         }
     }
@@ -54,7 +54,7 @@ public class InitialSetup {
         if (!GeneralUtils.isValidUUID(secretKey)) {
             // Generating a random UUID as the secret key
             secretKey = UUID.randomUUID().toString();
-            GeneralUtils.saveKeyToConfig("AutomaticallyGenerated.key", secretKey);
+            GeneralUtils.saveKeyToSettings("AutomaticallyGenerated.key", secretKey);
             applicationProperties.getAutomaticallyGenerated().setKey(secretKey);
         }
     }
@@ -64,8 +64,8 @@ public class InitialSetup {
                 "0.36.0", applicationProperties.getAutomaticallyGenerated().getAppVersion())) {
             Boolean csrf = applicationProperties.getSecurity().getCsrfDisabled();
             if (!csrf) {
-                GeneralUtils.saveKeyToConfig("security.csrfDisabled", false, false);
-                GeneralUtils.saveKeyToConfig("system.enableAnalytics", "true", false);
+                GeneralUtils.saveKeyToSettings("security.csrfDisabled", false);
+                GeneralUtils.saveKeyToSettings("system.enableAnalytics", true);
                 applicationProperties.getSecurity().setCsrfDisabled(false);
             }
         }
@@ -76,14 +76,14 @@ public class InitialSetup {
         String termsUrl = applicationProperties.getLegal().getTermsAndConditions();
         if (StringUtils.isEmpty(termsUrl)) {
             String defaultTermsUrl = "https://www.stirlingpdf.com/terms-and-conditions";
-            GeneralUtils.saveKeyToConfig("legal.termsAndConditions", defaultTermsUrl, false);
+            GeneralUtils.saveKeyToSettings("legal.termsAndConditions", defaultTermsUrl);
             applicationProperties.getLegal().setTermsAndConditions(defaultTermsUrl);
         }
         // Initialize Privacy Policy
         String privacyUrl = applicationProperties.getLegal().getPrivacyPolicy();
         if (StringUtils.isEmpty(privacyUrl)) {
             String defaultPrivacyUrl = "https://www.stirlingpdf.com/privacy-policy";
-            GeneralUtils.saveKeyToConfig("legal.privacyPolicy", defaultPrivacyUrl, false);
+            GeneralUtils.saveKeyToSettings("legal.privacyPolicy", defaultPrivacyUrl);
             applicationProperties.getLegal().setPrivacyPolicy(defaultPrivacyUrl);
         }
     }
@@ -97,7 +97,7 @@ public class InitialSetup {
             appVersion = props.getProperty("version");
         } catch (Exception e) {
         }
+        GeneralUtils.saveKeyToSettings("AutomaticallyGenerated.appVersion", appVersion);
         applicationProperties.getAutomaticallyGenerated().setAppVersion(appVersion);
-        GeneralUtils.saveKeyToConfig("AutomaticallyGenerated.appVersion", appVersion, false);
     }
 }