docs(skill): correct upstream-sync file mapping and add omit-vs-null pitfall

[krukow]

_{Generated via Copilot on behalf of @krukow}

Phase 10 self-review of the update-upstream skill, following the v1.0.0-beta.12 sync (#115). Documentation-only — corrects drift between the skill's reference material and the actual codebase.

Changes

• AGENTS.md (.github/copilot-instructions.md) — the Project Structure tree was missing two real files: tool_set.clj and the top-level public namespace src/github/copilot_sdk.clj (home of the curated public event-types / session-events sets that sync work depends on).
• references/PROJECT.md — the upstream↔Clojure mapping pointed the public event-types set at client.clj (it lives in copilot_sdk.clj) and referenced a non-existent subscribe-events!. Corrected, split the curated-vs-generated event sets into distinct rows, and added the toolSet.ts → tool_set.clj mapping.
• SKILL.md — adds pitfall [docs] Populate documentation.instructions.md for AI agents #5: outbound optional wire fields must match upstream's omit-vs-null behavior per RPC. The contextTier lesson from Upstream sync: copilot-sdk v1.0.0-beta.12 (schema 1.0.57) #115, generalized — compute the wire value and gate on (some? v) when the request schema has no null variant (e.g. session.model.switchTo), rather than contains?-gating and emitting JSON null.

Validation

bb validate-docs ✓ (13 files, 0 warnings). No source or test changes.

[Copilot]

Pull request overview

Documentation-only update to the update-upstream skill reference material, correcting drift between the skill docs and the current codebase (notably around event set locations and tool filtering), and capturing a recurring wire-level pitfall (omit vs null for optional RPC fields).

Changes:

• Add a new “omit-vs-null” pitfall for outbound optional RPC fields, with guidance to mirror upstream undefined-omission semantics when schemas don’t allow null.
• Fix the upstream↔Clojure mapping to point curated public event sets at src/github/copilot_sdk.clj, distinguish curated vs generated event sources, and add the toolSet.ts → tool_set.clj mapping.
• Update the project-structure listing used by Copilot instructions to include src/github/copilot_sdk.clj and tool_set.clj.

Show a summary per file

File	Description
.github/skills/update-upstream/SKILL.md	Adds a concrete, generalized pitfall about omitting optional wire fields vs emitting JSON null, aligned with upstream behavior and schema unions.
.github/skills/update-upstream/references/PROJECT.md	Corrects sync mapping for curated event sets and tool filtering helpers; removes references to non-existent APIs and clarifies generated vs curated event sources.
.github/copilot-instructions.md	Brings the documented project structure in line with the actual src/ layout by listing the top-level public namespace file and tool_set.clj.

Copilot's findings

• Files reviewed: 3/3 changed files
• Comments generated: 0