add agent skills structure used new structure to create compound structure PRD + issues

[JohnRushKucharski]

Extra structures for copilot skills.

[Copilot]

Pull request overview

This PR adds repository-local “agent skills” documentation under .github/skills/, along with supporting repo context docs (CONTEXT.md, AGENTS.md, PRD) and several example ribasim.toml configs for docs/tutorial datasets.

Changes:

• Added a structured set of agent skill instructions (triage, TDD, diagnose, fix-issue, PRD/issues breakdown, etc.) under .github/skills/.
• Added domain/context and process documentation (CONTEXT.md, AGENTS.md, issue-tracker/labels docs) plus a first PRD for Compound Structures (MVP).
• Added ribasim.toml files to multiple docs datasets (guide + crystal-basin tutorial).

Reviewed changes

Copilot reviewed 37 out of 117 changed files in this pull request and generated 16 comments.

Show a summary per file

File	Description
docs/tutorial/crystal-basin/Crystal-1/ribasim.toml	Adds tutorial model config (time window, CRS, I/O dirs, version).
docs/tutorial/crystal-basin/Crystal-2/ribasim.toml	Adds tutorial model config (time window, CRS, I/O dirs, version).
docs/tutorial/crystal-basin/Crystal-3/ribasim.toml	Adds tutorial model config (time window, CRS, I/O dirs, version).
docs/guide/data/basic/ribasim.toml	Adds basic guide dataset config.
docs/guide/data/level_range/ribasim.toml	Adds guide dataset config + solver tolerances section.
docs/guide/data/local_pidcontrolled_cascade/ribasim.toml	Adds guide dataset config.
docs/guide/data/outlet_continuous_control/ribasim.toml	Adds guide dataset config.
docs/guide/data/pid_control/ribasim.toml	Adds guide dataset config.
CONTEXT.md	Introduces domain glossary/context for “Compound Structure”, Nodes, Links, protocol concepts.
AGENTS.md	Adds an entrypoint doc pointing to issue tracker/labels/domain docs.
.github/skills/zoom-out/SKILL.md	Adds a “zoom-out” skill prompt.
.github/skills/triage/SKILL.md	Adds an issue triage workflow skill (roles, state machine, templates).
.github/skills/triage/OUT-OF-SCOPE.md	Documents out-of-scope knowledge base conventions for triage.
.github/skills/triage/AGENT-BRIEF.md	Adds guidance/template for writing durable agent briefs.
.github/skills/to-prd/SKILL.md	Adds a skill to synthesize a PRD from conversation context.
.github/skills/to-issues/SKILL.md	Adds a skill to break plans/PRDs into vertical-slice issues.
.github/skills/tdd/tests.md	Adds examples of good/bad tests for the TDD skill.
.github/skills/tdd/SKILL.md	Adds the TDD workflow guidance (vertical slices, red/green/refactor).
.github/skills/tdd/refactoring.md	Adds refactor-candidate checklist for TDD loop.
.github/skills/tdd/mocking.md	Adds mocking guidance (mock only at system seams).
.github/skills/tdd/interface-design.md	Adds testability-focused interface design guidance.
.github/skills/tdd/deep-modules.md	Adds deep-module vs shallow-module guidance.
.github/skills/ralph-loop/SKILL.md	Adds orchestration skill for looping over “ready-for-agent” issues.
.github/skills/improve-codebase-architecture/SKILL.md	Adds architecture improvement skill using shared vocabulary.
.github/skills/improve-codebase-architecture/LANGUAGE.md	Defines the required architecture vocabulary for that skill.
.github/skills/improve-codebase-architecture/INTERFACE-DESIGN.md	Adds a “design it twice” interface exploration process.
.github/skills/improve-codebase-architecture/DEEPENING.md	Adds dependency categories + testing strategy for deepening.
.github/skills/grill-with-docs/SKILL.md	Adds a “grill-with-docs” interviewing + inline-doc-update skill.
.github/skills/grill-with-docs/CONTEXT-FORMAT.md	Defines expected CONTEXT.md format for grilling sessions.
.github/skills/grill-with-docs/ADR-FORMAT.md	Defines ADR format/location guidance for grilling sessions.
.github/skills/fix-issue/SKILL.md	Adds an end-to-end AFK issue fixing workflow skill.
.github/skills/diagnose/SKILL.md	Adds a disciplined diagnosis workflow skill.
.github/skills/diagnose/scripts/hitl-loop.template.sh	Adds a human-in-the-loop repro loop script template.
.github/prd/0001-compound-structures-mvp.md	Adds the first PRD document for Compound Structures MVP.
.github/agents/triage-labels.md	Adds canonical triage-role → label mapping doc.
.github/agents/issue-tracker.md	Documents issue tracker operations and conventions (gh CLI).
.github/agents/domain.md	Documents how skills should consume domain docs + ADRs.

[Copilot]

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