feat: add built-in help system with fuzzy search for INPUT parameters (#6935)

* feat: add built-in help system with fuzzy search for INPUT parameters

- Add -h/--help flag for parameter documentation
- Add -s/--search flag for keyword search
- Implement fuzzy matching for typo suggestions (Levenshtein distance)
- Case-insensitive parameter lookup
- Auto-generate help data from markdown at build time
- 458 parameters documented with comprehensive metadata

Usage: abacus -h <param>, abacus -s <keyword>

refactor(help): improve help system with critical fixes and performance optimizations

docs(help): integrate help system documentation into quick start guide

Add concise help system section to docs/quick_start/input.md covering:
- Basic commands (-h, -s flags)
- Example output for parameter lookup
- Fuzzy matching for typo suggestions
- Case-insensitive lookup behavior

Remove standalone documentation files that are now redundant:
- docs/HELP_SYSTEM.md
- docs/FUZZY_SEARCH.md

* fix(test): fix help system unit tests

- Add input_help.cpp to MODULE_IO_parse_args test sources to fix linker error
- Fix input_help_test.cpp include path and use value syntax instead of pointer
- Fix parse_args_test.cpp death tests to use EXPECT_EXIT regex matching
  instead of CaptureStderr which doesn't work properly with fork()

* refactor(help): address PR review feedback and improve fuzzy matching

This commit addresses all code review comments and fixes a critical UX issue
in the help system's fuzzy matching algorithm.

## Documentation Fixes
- Fix incorrect "case-sensitive" documentation (should be "case-insensitive")
- Update API documentation for find_similar_parameters() with new algorithm details
- Add inline comments explaining 3-tier matching strategy

## Architecture Improvements
- Add std::ostream& parameter to show_general_help() and show_parameter_help()
- Enable flexible stream redirection (stdout for success, stderr for errors)
- Maintain backward compatibility with default parameters
- Eliminate code duplication by reusing show_general_help() in error handler

## UX Fix: Fuzzy Matching Algorithm

### Problem
Pure Levenshtein distance suggested semantically irrelevant parameters:
- "abacus -h relax" incorrectly suggested "dmax" and "nelec"

### Solution
Implement 3-tier semantic matching strategy:
1. Prefix matches (e.g., "relax" → "relax_new") - Priority 0
2. Substring matches (e.g., "cut" → "ecutwfc") - Priority 1
3. Levenshtein distance for typos - Priority 10+

* feat(docs): auto-generate INPUT docs from C++ source with built-in help system

Migrate INPUT parameter documentation from a manually-maintained markdown
file to auto-generation from C++ source. Documentation fields (category,
type, description, default_value, unit, availability) are now embedded
directly in Input_Item registrations in read_input_item_*.cpp files,
serving as the single source of truth for both the built-in --help system
and the Sphinx documentation.

Key changes:
- Add docs/generate_docs_from_source.py to parse C++ source and generate
  input-main.md (492 parameters across 34 categories)
- Hook generator into Sphinx build via builder-inited event in conf.py
- Add [NOTE] documentation to 36 parameters preserving notes from the
  previous manually-maintained docs (version compat, usage caveats)
- Fix generator regex to handle comments before Input_Item declarations
- Rename tmp_item to item in smearing_sigma_temp block for generator
  compatibility
- Remove old tools/generate_help_data.py and input_help_data.h pipeline

* feat(docs): replace regex-based doc generation with YAML pipeline

The old generate_docs_from_source.py parsed C++ source files with regex
to extract Input_Item metadata, which was fragile and broke on code
refactoring. Replace it with a pipeline that uses the binary's own
parameter registry:

  abacus --generate-parameters-yaml > docs/parameters.yaml
  python docs/generate_input_main.py docs/parameters.yaml

- Add ParameterHelp::generate_yaml() with YAML serialization helpers
- Add --generate-parameters-yaml CLI flag to parse_args.cpp
- Add POST_BUILD command in CMakeLists.txt to auto-regenerate
  docs/parameters.yaml on every build
- Create docs/generate_input_main.py (YAML-to-markdown converter)
- Update docs/conf.py Sphinx hook to use YAML pipeline
- Track docs/parameters.yaml in the repository
- Delete docs/generate_docs_from_source.py
- Add 5 unit tests for YAML generation

* fix(docs): quote numeric YAML values, remove auto-generation, update contributing guide

- Quote numeric-looking default values in yaml_quote_if_needed() so
  PyYAML parses them as strings (fixes 92 parameters losing defaults)
- Also quote .inf, -.inf, .nan YAML special values
- Fix Python generate_input_main.py to use != '' instead of truthiness
  checks, preventing falsy-but-valid values (e.g. 0) from being dropped
- Replace sys.exit(1) with FileNotFoundError in generate() for safe use
  as a library from conf.py
- Remove POST_BUILD command from CMakeLists.txt (not portable across
  CMake generators, breaks cross-compilation)
- Update CONTRIBUTING.md "Documenting INPUT Parameters" section to
  describe the YAML-based workflow and remind developers to regenerate
  docs/parameters.yaml when adding or modifying parameters
- Regenerate docs/parameters.yaml with all values properly quoted

* fix(docs): reorder add_item() calls in read_input_item_*.cpp to match legacy doc order

The built-in help system generates input-main.md from C++ source, with
parameter order determined by add_item() call order. After introducing
the YAML-based doc pipeline, 19 of 32 documentation sections had
different parameter ordering compared to the old hand-maintained
input-main.md.

Reorder item blocks within each of the 13 read_input_item_*.cpp files
to restore the original documentation order. This is a pure mechanical
reordering with no logic changes. 28 of 32 sections now match; the
4 remaining differences are due to cross-file constraints (constructor
call order) that cannot be resolved without moving items between files.

Add a comment to each item_*() function noting that add_item() call
order determines generated documentation order.

* Add pyyaml as requirements for documentation generation

* Commit updated input-main.md and parameters.yaml

* Commit the changes to the parameters.yaml

* fix(input): restore develop-parity token count handling for read_input output items

Author: zhubonan

docs/CONTRIBUTING.md

@@ -10,6 +10,7 @@ For more non-technical aspects, please refer to the [ABACUS Contribution Guide](
 - [Structure of the package](#structure-of-the-package)
 - [Submitting an Issue](#submitting-an-issue)
 - [Comment style for documentation](#comment-style-for-documentation)
+- [Documenting INPUT parameters](#documenting-input-parameters)
 - [Code formatting style](#code-formatting-style)
 - [Generating code coverage report](#generating-code-coverage-report)
 - [Adding a unit test](#adding-a-unit-test)
@@ -156,6 +157,72 @@ An practical example is class [LCAO_Deepks](https://github.com/deepmodeling/abac
     \f}
     ```
 
+## Documenting INPUT Parameters
+
+ABACUS includes a built-in help system that allows users to query INPUT parameters directly from the command line (e.g., `abacus -h ecutwfc`). Parameter metadata is defined inline in the C++ source files (`source/source_io/module_parameter/read_input_item_*.cpp`) using `Input_Item` registrations.
+
+A checked-in file `docs/parameters.yaml` contains a YAML dump of all parameter metadata, generated from the binary itself. This file is used by Sphinx to produce the online documentation page `input-main.md`.
+
+### When to Update `docs/parameters.yaml`
+
+You **must** regenerate `docs/parameters.yaml` whenever you:
+
+- Add a new INPUT parameter
+- Remove an existing INPUT parameter
+- Change a parameter's description, type, default value, unit, category, or availability
+
+### How to Regenerate
+
+After building ABACUS, run:
+
+```bash
+./build/abacus --generate-parameters-yaml > docs/parameters.yaml
+```
+
+Then verify the YAML is valid:
+
+```bash
+python3 -c "import yaml; d=yaml.safe_load(open('docs/parameters.yaml')); print(len(d['parameters']), 'parameters')"
+```
+
+You can also regenerate the markdown documentation locally:
+
+```bash
+python3 docs/generate_input_main.py docs/parameters.yaml --output docs/advanced/input_files/input-main.md
+```
+
+**Important:** Include the updated `docs/parameters.yaml` in your commit when submitting a PR that modifies INPUT parameters. Reviewers should verify the YAML changes match the C++ source changes.
+
+### Parameter Documentation Format
+
+When adding or modifying INPUT parameters in C++ source, set the following fields on the `Input_Item`:
+
+```cpp
+{
+    Input_Item item("my_parameter");
+    item.category = "System variables";
+    item.type = "Integer";
+    item.description = "Description of what this parameter does.";
+    item.default_value = "0";
+    item.unit = "Ry";          // Optional, empty string if no unit
+    item.availability = "";    // Optional, empty string if always available
+    // ... read_value, reset_value, check_value functions ...
+    this->add_item(item);
+}
+```
+
+Supported types: `Integer`, `Real`, `String`, `Boolean`
+
+### Format Validation
+
+After regenerating the YAML, you can spot-check a specific parameter:
+
+```bash
+./build/abacus -h my_parameter
+```
+
+This uses the same runtime registry that generates the YAML, so if the help output looks correct, the YAML will be correct too.
+
 ## Code formatting style
 
 We use `clang-format` as our code formatter. The `.clang-format` file in root directory describes the rules to conform with.