SugarDetectionUtility integration and re-work of input file type detection (enhanced SMILES file parsing)

[JonasSchaub]

fixes #15
Updates CDK to v 2.12-SNAPSHOT (to get the SDU)
Preparation for v 1.6

[sonarqubecloud]

Quality Gate failed

Failed conditions
C Reliability Rating on New Code (required ≥ A)

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[Copilot]

Pull Request Overview

This PR integrates the SugarDetectionUtility (SDU) from CDK v2.12-SNAPSHOT and reworks input file type detection with enhanced SMILES file parsing capabilities. The main purpose is to prepare for version 1.6 by incorporating advanced sugar detection and processing functionality while improving file format recognition.

Key changes include:

• Addition of comprehensive SMILES file format detection and parsing capabilities
• Integration of SugarDetectionUtility for advanced sugar detection and processing
• Refactoring of test files to use proper CDK package structure
• Enhancement of existing SugarRemovalUtility tests with new functionality

Reviewed Changes

Copilot reviewed 20 out of 21 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
Test SMILES files	Added various test files with different formats for dynamic SMILES reading
SugarRemovalUtilityTest.java	Updated package structure and added comprehensive sugar detection tests
SugarDetectionUtilityTest.java	New comprehensive test suite for sugar detection functionality
DynamicSMILESFileReaderTest.java	Test suite for enhanced SMILES file format detection
SMILESFormatMatcher.java	Removed CDK book example class
DynamicSMILESFileReader.java	New dynamic SMILES file reader with format detection
DynamicSMILESFileFormat.java	Data structure for SMILES file format specification

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