Add citation info, supported supercomputer list, and documentation fixes

[k-yoshimi]

Summary

• Citation: Add a Citation section (paper reference + BibTeX) to README and the ja/en manuals for Yoshimi et al., STAM: Methods 5, 2564055 (2025).
• Supported systems: List supercomputers where moller is pre-installed (ISSP kugui/ohtaka, Tohoku Univ. AOBA, Kyushu Univ. Genkai) and note that Miyabi (ITC, Univ. of Tokyo) is supported with pre-installation in progress (as of Aug 14, 2026). Each entry links to the system's website (English pages in English documents). Per-machine usage details are intentionally not documented; readers are directed to each system's user guide.
• Acknowledgment: Note that the Miyabi/Genkai installations were supported by JST Moonshot R&D Program (Grant Number JPMJMS24A3).
• License notation: Unify to GPL-3.0-or-later across README and manuals (consistent with pyproject.toml).
• File-format reference: Document the pbs and default values of the system parameter in addition to ohtaka/kugui.
• Manual cleanup: Fix typos (Instutite→Institute, Corrdinator→Coordinator, paralle→parallel, betch→batch), a broken inline literal, a duplicate Sphinx label (sec-tutorial in the ja tutorial), and tab characters in YAML examples. Both ja/en manuals now build with zero Sphinx warnings.
• Add CLAUDE.md with repository guidance for Claude Code.

Verification

• make -C docs/en html and make -C docs/ja html succeed with no warnings; make latexpdf also builds for both languages.
• All external links verified to return HTTP 200.
• Reviewed with ai-review-cycle (docs/workflow reviewer); remaining suggestion (per-machine system: values) is intentionally omitted due to the confidentiality policy above.

🤖 Generated with Claude Code

https://claude.ai/code/session_012Ar4PAN3bT9pEL8rj8txNc

[Copilot]

Pull request overview

This PR updates moller’s user-facing documentation to include formal citation information, clarify supported/pre-installed supercomputer environments, and fix a set of typos / Sphinx formatting issues (including removing a duplicate Sphinx label). It also adds a CLAUDE.md repository guidance file.

Changes:

• Add citation text + BibTeX entry to the top-level README and both JA/EN manuals, and add an acknowledgment for supported installations.
• Document additional accepted system values (pbs, default) in the file-format reference and clean up YAML example formatting (tabs/indentation).
• Fix documentation typos and Sphinx issues (broken inline literal, duplicate sec-tutorial label).

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
sample/moller/simple/README.md	Fixes a typo (“paralle” → “parallel”) in the sample README.
README.md	Adds supported/pre-installed system list, acknowledgement, citation section, and unifies license wording to GPL-3.0-or-later.
docs/ja/source/moller/tutorial/index.rst	Removes duplicate sec-tutorial label to eliminate Sphinx warning.
docs/ja/source/moller/tutorial/basic.rst	Fixes typo in parameter description (paralle → parallel).
docs/ja/source/moller/filespec/index.rst	Documents pbs/default for system and cleans YAML example indentation/tabs.
docs/ja/source/moller/about/index.rst	Adds license notation clarification, citation section, acknowledgments, and pre-installed system list (JA).
docs/en/source/moller/tutorial/basic.rst	Fixes broken inline literal around output.
docs/en/source/moller/filespec/index.rst	Fixes typo (“betch” → “batch”), documents pbs/default, and cleans indentation/tabs in examples.
docs/en/source/moller/about/index.rst	Fixes typos, clarifies license notation, adds citation + acknowledgment, and lists pre-installed systems (EN).
CLAUDE.md	Adds repository architecture/maintenance guidance for Claude Code usage in this repo.

---

💡 Add a code-review agent skill or configure MCP servers for context-aware, tailored reviews. Learn more in the docs.