docs: clarify mode descriptions and agent writing guidance

[MarcusKainth]

What this changes, and why

AGENTS.md introduces only emulation mode and ambiguously applies its comment rules to commit messages. Describe both emulation and native mode, and clarify that commits carry rationale and relevant history while comments describe the current code. CLAUDE.md links to AGENTS.md, so both tools receive the same guidance.

Evidence

$ git diff origin/main...HEAD --stat
 AGENTS.md | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

$ git diff --check origin/main...HEAD
(no output; exit 0)

Invariants

None. No PUR-N rule or implementation changes.

Spec impact

• None. SPEC.md, NATIVE.md and PURITY.md are unchanged.

Checks

• make gates: incomplete as documented above.
• No AI attribution trailers in the commits.

Anything else

Written mostly by Codex.