chore: move skills and evals to plugins/bin, remove legacy root configs

Skills and evals migrated from .agents/ to plugins/bin/ plugin directory.
Remove .mcp.json, provider-manifest.sh, and skills-lock.json legacy artifacts.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

plugins/bin/skills/research/SKILL.md

@@ -0,0 +1,97 @@
+---
+name: research
+description: >-
+  Use when the user wants to research a topic and generate structured reference
+  markdown files. Handles: finding canonical docs for a tool/library/API via
+  Context7 MCP or web sources, reading and deepening into linked pages,
+  organizing extracted content into topic files (overview, installation,
+  configuration, cli-reference, api-reference, examples, troubleshooting). Do
+  NOT use when the user wants to write documentation from existing code or specs
+  (use write-docs), install or manage the neuledge-context MCP server (use
+  neuledge-context), or research a bug/incident (use diagnose).
+metadata:
+  category: research
+allowed-tools:
+  - WebSearch
+  - WebFetch
+  - Read
+  - Write
+  - mcp__context7__resolve-library-id
+  - mcp__context7__query-docs
+model: sonnet
+---
+
+<requirements>
+
+## Required inputs
+
+- **Topic** — the subject to research (tool, library, API, concept); inferred from user description if clear, ask if ambiguous
+- **Output path** — directory where reference files will be written; must be provided explicitly — do not infer or default
+- **Starting URLs** — optional; if provided, skip discovery websearch and read these first
+
+## Constraints
+
+- Never write files outside the explicitly provided output path
+- Skip any default topic file if no relevant content is found for it — do not create empty files
+- Create additional topic files beyond the default list when content warrants it (e.g. `webhooks.md`, `rate-limits.md`)
+- Subagents handle parallel source reading and link deepening — the orchestrator writes all files; subagents return summaries only, never write directly
+- Context7 MCP calls (`resolve-library-id`, `query-docs`) are made only by the orchestrator at step 2 — subagents must not call them
+- `sources.md` is always written, even if only one source was read
+- Each topic file must have frontmatter with `topic` and `source_keys`; body is prose only — no inline URLs
+- Source keys in `sources.md` must be kebab-case slugs: derived from the source domain or page title for web sources; for Context7 sources use `context7-<library-slug>` (e.g. `context7-vercel-next-js`)
+- Default topic list and file format spec live in `references/` sub-files — read them at step 1
+
+</requirements>
+
+<steps>
+
+## Process
+
+1. **Scan codebase.** Search the working directory for existing usage of the topic — imports, config files, version pins, existing reference files. Use findings to narrow research scope (e.g. target the version already in use, skip topics already documented). Read `references/topics.md` for the default topic list and `references/file-format.md` for the output file format spec.
+
+2. **Try Context7.** If the topic is a library, framework, or API and no starting URLs were provided, call `resolve-library-id` with the topic name and the user's question. If a match resolves, call `query-docs` once per default topic area (see `references/topics.md`). Treat each response as a source summary with slug `context7-<library-slug>` (e.g. `context7-vercel-next-js`). A topic area has sufficient content when the Context7 response contains at least one substantive paragraph — not a "no results" message, redirect notice, or header-only boilerplate. Mark covered topic areas — skip their subagent web reads in step 4. If the library does not resolve, or starting URLs were provided (explicit source choice by the user), skip this step entirely.
+
+3. **Discover sources.** For topics not covered by Context7 (or when no starting URLs were provided and Context7 did not resolve), websearch for canonical documentation (prefer `llms.txt`, developer docs, official API references over tutorials or blog posts). Collect 3–5 candidate URLs before reading any.
+
+4. **Read sources in parallel.** Spawn one subagent per source URL. Each subagent fetches the page, extracts relevant content, identifies links worth deepening, and returns a structured summary (content by topic area + links to follow). Subagents do not write files.
+
+5. **Deepen.** For each subagent that returned links worth following, spawn child subagents per branch. Continue until content becomes repetitive or out of scope. Cap at ~10 additional pages total across all branches.
+
+6. **Consolidate.** Merge all subagent summaries (Context7 and web) by topic area. Identify which default topics have sufficient content and which custom topics emerged.
+
+7. **Write topic files.** For each topic with content, write `<output-path>/<topic>.md` using the format in `references/file-format.md`. Orchestrator writes all files — never delegate file writing to a subagent.
+
+8. **Write `sources.md`.** Write `<output-path>/sources.md` mapping each source slug to its URL (use `context7:<library-id>` as the URL for Context7 sources), description, and list of topic files it contributed to. Include sources that yielded no content, marked `no content extracted`.
+
+## Output format
+
+- `<output-path>/<topic>.md` per topic with content — formatted per `references/file-format.md`
+- `<output-path>/sources.md` — always produced; maps slug → URL, description, contributing files
+
+</steps>
+
+<checks>
+
+## Failure handling
+
+- Output path not provided — stop and ask; do not infer or default
+- No sources found after websearch — report what was searched, ask user to provide starting URLs
+- Subagent returns no usable content — skip that source, log in `sources.md` as `no content extracted`
+- All topic files would be empty — stop, report what was searched, do not write any files
+
+## Self-check
+
+- [ ] Codebase scanned before any websearch was performed
+- [ ] Output path was explicitly provided — not inferred
+- [ ] `references/topics.md` and `references/file-format.md` read at step 1
+- [ ] Context7 resolution attempted before websearch when topic is a library/framework/API
+- [ ] Context7 calls made only at orchestrator step 2 — no subagent called `resolve-library-id` or `query-docs`
+- [ ] Context7 sources recorded in `sources.md` with `context7:<library-id>` as URL
+- [ ] No topic file written without content
+- [ ] `sources.md` written with all sources read (including those with no content extracted)
+- [ ] All file writes performed by the orchestrator, not subagents
+- [ ] Each topic file has `topic` and `source_keys` frontmatter fields
+- [ ] All source keys in topic files have a matching entry in `sources.md`
+- [ ] No files written outside the provided output path
+
+</checks>