Add atst examples in ASE interfaces examples

[QuantumMisaka]

Reminder

• I have read AGENTS.md and docs/developers_guide/agent_governance.md.
• I have linked an issue or explained why this PR does not need one.
• I have added adequate unit tests and/or case tests, or explained why not.
• I have listed the exact verification commands run and their results.
• I have described user-visible behavior changes, including INPUT parameter changes.
• I have explained core-module impact for ESolver, HSolver, ElecState, Hamilt, Operator, Psi, or other source/ changes.
• No governance exception is requested.

Linked Issue

No linked issue. This PR refines documentation discovery for the optional external ATST-Tools transition-state workflow project.

Unit Tests and/or Case Tests for my changes

No new unit or case test is added. The final diff is documentation-only and changes no ABACUS or abacuslite runtime behavior.

Exact Verification Performed

• git diff --check c43b14edff0867b41d18a8caa83b83ed18c07ade HEAD: passed.
• git diff --name-only c43b14edff0867b41d18a8caa83b83ed18c07ade HEAD: passed; output contains only interfaces/ASE_interface/README.md.
• python3 tools/03_code_analysis/agent_governance_check.py --base c43b14edff0867b41d18a8caa83b83ed18c07ade --head HEAD --format text: passed with Agent governance check: no findings.
• Prohibited-content scan confirmed that the README contains no ATST CLI command, installation command, YAML snippet, or Python import: passed.
• HTTP HEAD checks for the ATST-Tools repository, ABACUSLite Wrapper Guide, and ABACUS-backed NEB example: all returned HTTP 200.
• Checks not run: ABACUS build, numerical runtime, and ATST runtime checks. They are not applicable because the final PR changes only a README discovery entry and contains no executable ATST content.

What's changed?

• Removes all previously added interfaces/ASE_interface/examples/atst_tools/ files, including ATST YAML configurations and helper scripts.
• Replaces the local example-tree entry with a concise Advanced optional workflows README section.
• Links readers to the independently maintained ATST-Tools repository, its ABACUSLite Wrapper Guide, and an ABACUS-backed NEB example.
• States that ATST-Tools is optional, can use abacuslite as an ABACUS ASE calculator backend, and is not an ABACUS or abacuslite dependency.

Why this scope?

ATST-Tools owns its installation, CLI, configuration schema, runnable workflows, and validation. Keeping those files in its own repository avoids adding an operational or maintenance dependency to ABACUS while preserving a clear discovery path for advanced ASE transition-state workflows.

Governance Checklist

• Global dependencies: no GlobalV, GlobalC, or PARAM references are added.
• Dependencies: no package, build, CMake, test, CI, or environment dependency is added.
• Default parameters and headers: no interface or header changes.
• Build linkage: no source files are added or changed.
• Line endings: changed text uses LF.
• Documentation: only the abacuslite README is changed.

INPUT Parameter Changes

• Parameters added/removed/changed: none.
• docs/parameters.yaml updated: not applicable.
• docs/advanced/input_files/input-main.md updated: not applicable.

Core Module Impact

• Affected core modules: none.
• Compatibility or performance impact: none expected.

Governance Exception

• Rule: none.
• Reason: not applicable.
• Scope: not applicable.
• User or maintenance risk: not applicable.
• Why the normal rule cannot be followed now: not applicable.
• Follow-up cleanup plan: not applicable.
• Requested approver: not applicable.

[kirk0830]

this PR tries to show the usage to interface with the ATST-Tools, which is the package collects some sophisticated algorithms that can widen the scope of ABACUS usage. However, the introduced dependency is unacceptable, the change proposed on the file structure is also to be corrected.

[kirk0830]

1. Regarding the interface selection between ATST API and input file driven mode:
From the maintenance perspective, the programmatic Python API interface provides better long-term stability compared with static input files. We recommend prioritizing the Python API approach rather than combining input files with wrapper scripts. Maintaining a single API-based Python script will greatly reduce ongoing maintenance burden; it also simplifies future PR reviews and diff tracking for this module.
​
2. For documentation and header comments of the example script:
If you intend to mention ATST CLI mode in this example file, please add a comprehensive docstring at the very top of the script with following structured information:

• Purpose and scope of this demonstration example
  ​
• ATST installation instructions with official link
  ​
• Brief overview of ATST capabilities, together with official documentation link for CLI usage
  After the header documentation block, implement the logic via  from atst import xxx  API calls consistently.

3. Redundant example contents need pruning:
Please remove duplicated demonstrations for generic functionalities, such as conventional geometry optimization (non-P-RFO variants) and standard NEB calculations. These are not ATST-specific features and result in redundant code. This example file should only showcase unique, distinctive capabilities native to ATST in a single concise script.