refactor(algorithm,io,system): modularize monolithic files into focused subdirectories

## Changes
- algorithm: Decompose monolithic headers (algorithm.hpp, base.hpp, bignumber.hpp, blowfish.hpp, convolve.hpp, etc.) into domain-specific subdirectories (encoding/, crypto/, hash/, math/, signal/, graphics/, optimization/, utils/, core/)
- algorithm: Add new modules — bloom_filter, boyer_moore, kmp, rust_types, xor_cipher, xtea/xxtea, base32/base64/hex/url encoding, convolution, edge_detection, perlin_opencl, keccak, minhash, number_theory, parallel_math, safe_math, random
- io: Remove old monolithic headers (async_io.hpp, compress.hpp, async_compress.hpp, etc.) and reorganize into async/, compression/, core/, filesystem/ subdirectories
- io: Add new focused modules — async_batch, async_compressor, async_decompressor, async_directory, async_file, async_simd, async_stream, async_zip, backup, data_compress, gz_compress, slice_compress, zip_operations, directory_ops, file_ops, file_query, file_split_merge, path_convert
- system/clipboard: Remove old platform-specific monolithic files, refactor into focused modules (clipboard_async, clipboard_cache, clipboard_data, clipboard_image, clipboard_monitor, clipboard_query, clipboard_text)
- system/command: Extract async_executor, rate_limiter, resource_monitor, statistics, validation into separate files
- system/crontab: Extract batch operations, query, and type definitions into separate modules
- tests: Remove 7 old monolithic test files, update remaining tests to match new module structure
- examples: Update all examples to use new include paths
- python: Update all pybind11 bindings to match new module structure, enhance io bindings

## Files Changed
- 78 files in atom/algorithm/ (533+, 15675-)
- 30 files in atom/io/ (700+, 10690-)
- 31 files in atom/system/ (521+, 4727-)
- 23 files in tests/ (248+, 2377-)
- 45 files in example/ (1254+, 971-)
- 31 files in python/ (1633+, 449-)
- 177 new files added across all modules
- 55 old monolithic files deleted

## Details
Major architectural refactoring to improve code organization and maintainability.
Monolithic source files are decomposed into smaller, focused modules within
domain-specific subdirectories. This follows the single-responsibility principle
and makes the codebase easier to navigate, test, and extend independently.
Net reduction of ~30,000 lines through elimination of code duplication.

Author: AstroAir

atom/algorithm/CMakeLists.txt

@@ -26,95 +26,162 @@ find_package(TBB QUIET)
 # Sources and Headers
 set(SOURCES
     # Core files
-    core/algorithm.cpp
+    core/kmp.cpp
+    core/boyer_moore.cpp
     core/opencl_utils.cpp
     # Crypto files
     crypto/md5.cpp
     crypto/sha1.cpp
     crypto/blowfish.cpp
     crypto/tea.cpp
+    crypto/tea_common.cpp
+    crypto/xtea.cpp
+    crypto/xxtea.cpp
+    crypto/xor_cipher.cpp
     # Hash files
-    hash/mhash.cpp
+    hash/hex_utils.cpp
+    hash/keccak.cpp
+    hash/hash_context.cpp
+    hash/minhash.cpp
     # Math files
-    math/math.cpp
+    math/safe_math.cpp
+    math/bit_ops.cpp
+    math/number_theory.cpp
+    math/random.cpp
+    math/math_memory.cpp
+    math/parallel_math.cpp
     math/fraction.cpp
     math/bignumber.cpp
     math/gpu_math.cpp
     # Compression files
     compression/huffman.cpp
+    compression/huffman_optimized.cpp
     compression/matrix_compress.cpp
+    compression/matrix_compress_parallel.cpp
+    compression/matrix_compress_utils.cpp
     # Signal processing files
-    signal/convolve.cpp
+    signal/convolution_2d.cpp
+    signal/dft.cpp
+    signal/gaussian_filter.cpp
     # Optimization files
-    optimization/pathfinding.cpp
+    optimization/pathfinding/heuristics.cpp
+    optimization/pathfinding/grid_map.cpp
+    optimization/pathfinding/pathfinder.cpp
     # Encoding files
-    encoding/base.cpp
+    encoding/base64.cpp
+    encoding/base32.cpp
+    encoding/hex.cpp
+    encoding/url.cpp
     # Graphics files
     graphics/flood.cpp
     # Utils files
     utils/fnmatch.cpp)
 
 set(HEADERS
-    # Backwards compatibility headers (in root)
-    algorithm.hpp
-    annealing.hpp
-    base.hpp
-    bignumber.hpp
-    blowfish.hpp
-    convolve.hpp
-    error_calibration.hpp
-    flood.hpp
-    fnmatch.hpp
-    fraction.hpp
-    hash.hpp
-    huffman.hpp
-    math.hpp
-    matrix.hpp
-    matrix_compress.hpp
-    md5.hpp
-    mhash.hpp
-    pathfinding.hpp
-    perlin.hpp
-    rust_numeric.hpp
-    sha1.hpp
-    snowflake.hpp
-    tea.hpp
-    weight.hpp
-    # Actual implementation headers (in subdirectories)
+    # Barrel export header
+    index.hpp
+    # Algorithm exception hierarchy
+    algorithm_exception.hpp
+    # Implementation headers (in subdirectories)
     core/algorithm.hpp
+    core/kmp.hpp
+    core/bloom_filter.hpp
+    core/boyer_moore.hpp
     core/rust_numeric.hpp
+    core/rust_types.hpp
+    core/rust_error.hpp
+    core/rust_result.hpp
+    core/rust_option.hpp
+    core/rust_range.hpp
+    core/rust_int_methods.hpp
+    core/rust_float_methods.hpp
+    core/rust_iter.hpp
     core/simd_utils.hpp
     core/opencl_utils.hpp
     core/hex_utils.hpp
     crypto/md5.hpp
     crypto/sha1.hpp
     crypto/blowfish.hpp
     crypto/tea.hpp
+    crypto/tea_common.hpp
+    crypto/xtea.hpp
+    crypto/xxtea.hpp
+    crypto/crypto_utils.hpp
+    crypto/xor_cipher.hpp
     hash/hash.hpp
+    hash/hash_base.hpp
+    hash/hash_compute.hpp
+    hash/hex_utils.hpp
+    hash/keccak.hpp
+    hash/hash_context.hpp
+    hash/minhash.hpp
     hash/mhash.hpp
     math/math.hpp
+    math/math_concepts.hpp
+    math/safe_math.hpp
+    math/bit_ops.hpp
+    math/number_theory.hpp
+    math/random.hpp
+    math/math_memory.hpp
+    math/parallel_math.hpp
     math/matrix.hpp
     math/fraction.hpp
     math/bignumber.hpp
     math/statistics.hpp
     math/numerical.hpp
     math/gpu_math.hpp
+    math/linear_solver.hpp
+    math/levenberg_marquardt.hpp
     compression/huffman.hpp
+    compression/huffman_optimized.hpp
     compression/matrix_compress.hpp
+    compression/matrix_compress_parallel.hpp
+    compression/matrix_compress_utils.hpp
     signal/convolve.hpp
+    signal/convolve_common.hpp
+    signal/convolution_1d.hpp
+    signal/convolution_2d.hpp
+    signal/convolution_filters.hpp
+    signal/dft.hpp
+    signal/frequency_domain.hpp
+    signal/gaussian_filter.hpp
     optimization/annealing.hpp
+    optimization/annealing/annealing_concept.hpp
+    optimization/annealing/cooling_schedule.hpp
+    optimization/annealing/simulated_annealing.hpp
+    optimization/annealing/tsp.hpp
     optimization/pathfinding.hpp
+    optimization/pathfinding/point.hpp
+    optimization/pathfinding/graph.hpp
+    optimization/pathfinding/heuristics.hpp
+    optimization/pathfinding/grid_map.hpp
+    optimization/pathfinding/pathfinder.hpp
     encoding/base.hpp
+    encoding/detail.hpp
+    encoding/base64.hpp
+    encoding/base32.hpp
+    encoding/hex.hpp
+    encoding/url.hpp
+    encoding/xor_cipher.hpp
     graphics/flood.hpp
     graphics/noise_base.hpp
     graphics/perlin.hpp
     graphics/simplex.hpp
     graphics/image_ops.hpp
+    utils/async_calibration.hpp
     utils/error_calibration.hpp
     utils/fnmatch.hpp
+    utils/levenberg_marquardt.hpp
+    utils/linear_solver.hpp
     utils/snowflake.hpp
-    utils/weight.hpp
+    utils/snowflake_exception.hpp
     utils/uuid.hpp
+    utils/weight.hpp
+    utils/weight_collection.hpp
+    utils/weight_common.hpp
+    utils/weight_sampler.hpp
+    utils/weight_selector.hpp
+    utils/weight_strategy.hpp
     # Common utilities
     common/concepts.hpp
     common/endian.hpp
@@ -172,5 +239,9 @@ install(
   DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/atom
   COMPONENT development)
 
-# Install headers
-install(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/atom/algorithm)
+# Install headers preserving subdirectory structure
+foreach(_header ${HEADERS})
+  get_filename_component(_dir ${_header} DIRECTORY)
+  install(FILES ${_header}
+          DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/atom/algorithm/${_dir})
+endforeach()

atom/algorithm/algorithm.hpp

@@ -59,6 +59,22 @@ class UtilsException : public AlgorithmException {
     using AlgorithmException::AlgorithmException;
 };
 
+/**
+ * @brief Exception class for cryptography-related errors
+ */
+class CryptoException : public AlgorithmException {
+public:
+    using AlgorithmException::AlgorithmException;
+};
+
+/**
+ * @brief Exception class for compression-related errors
+ */
+class CompressionException : public AlgorithmException {
+public:
+    using AlgorithmException::AlgorithmException;
+};
+
 // Convenience macros for throwing algorithm exceptions
 #define THROW_ALGORITHM_ERROR(...)                                            \
     throw atom::algorithm::AlgorithmException(ATOM_FILE_NAME, ATOM_FILE_LINE, \
@@ -80,6 +96,14 @@ class UtilsException : public AlgorithmException {
     throw atom::algorithm::UtilsException(ATOM_FILE_NAME, ATOM_FILE_LINE, \
                                           ATOM_FUNC_NAME, __VA_ARGS__)
 
+#define THROW_CRYPTO_ERROR(...)                                            \
+    throw atom::algorithm::CryptoException(ATOM_FILE_NAME, ATOM_FILE_LINE, \
+                                           ATOM_FUNC_NAME, __VA_ARGS__)
+
+#define THROW_COMPRESSION_ERROR(...)                  \
+    throw atom::algorithm::CompressionException(      \
+        ATOM_FILE_NAME, ATOM_FILE_LINE, ATOM_FUNC_NAME, __VA_ARGS__)
+
 }  // namespace atom::algorithm
 
 #endif  // ATOM_ALGORITHM_ALGORITHM_EXCEPTION_HPP

atom/algorithm/algorithm_exception.hpp

@@ -90,6 +90,18 @@ concept Hashable = requires(T t) {
     { std::hash<T>{}(t) } -> std::convertible_to<usize>;
 };
 
+/**
+ * @brief Concept for unsigned integral types.
+ */
+template <typename T>
+concept UnsignedIntegral = std::unsigned_integral<T>;
+
+/**
+ * @brief Concept for arithmetic types (integral or floating-point).
+ */
+template <typename T>
+concept Arithmetic = std::integral<T> || std::floating_point<T>;
+
 }  // namespace atom::algorithm
 
 #endif  // ATOM_ALGORITHM_COMMON_CONCEPTS_HPP