Document repository-specific AI coding guidance in AGENTS.md

[Alexander-Mitrofanov]

Martin Boss,

This adds a repository-root AGENTS.md so coding agents can follow IntaRNA's current build, scientific and contribution conventions. The guidance is based on the current master code, configuration, CI, tests and ChangeLog.

Fixes #247.

Changes

• Document the C++23 compiler and standard-library requirement, Autotools setup, dependency configuration, focused API tests and the full API/CLI regression command.
• Specify the existing Doxygen style and show a compilable example with declarations inside the class and short functions explicitly inline after the class definition in the header.
• Explain exactly how to update both the development summary and dated entries in ChangeLog; this PR updates both.
• Require separate implementation branches and PR descriptions covering the problem, changes and validation results.
• Record IntaRNA-specific constraints around sequence orientation, energy units, scientific regression tests, ownership, public headers and thread safety. Mark old phase-specific branch instructions in doc/refactor/ as historical.

Research before implementation

I reviewed the AGENTS.md format guidance, OpenAI's guidance on keeping repository instructions focused, instruction scope and discovery, and Doxygen's documentation-block reference. The resulting guide uses concrete repository commands and conventions, links to detailed sources, and makes validation proportional to the change.

Validation

• bash autotools-init.sh and ./configure --help: passed; bootstrap left tracked build/source files unchanged.
• Verified all eight local documentation links and every documented configure option.
• Both shell examples passed bash -n.
• Extracted the C++ header example unchanged, compiled and linked it from two translation units with GCC 13.3 using -std=c++23 -Wall -Wextra -pedantic-errors, and ran the result successfully.
• Reviewed the commands against Makefile.am, tests/Makefile.am, tests/data/Makefile.am and the current CI workflow.
• git diff --cached --check: passed.

Only AGENTS.md and ChangeLog change. The full IntaRNA build/regression suite was not run locally for this documentation-only PR; there are no runtime, build-system or dependency changes.