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Seth Hobson be57c0b2e3 feat: multi-harness plugin marketplace (Codex, Cursor, OpenCode, Gemini) (#541)
* feat(adapters): multi-harness framework + harness_portability eval dimension

Turn this Claude Code plugin marketplace into a generic agentic-harness
marketplace. Adapters under tools/adapters/ emit harness-native artifacts
for OpenAI Codex CLI, Cursor, OpenCode, and Gemini CLI from a single
Markdown source. Source-of-truth stays under plugins/ — Claude Code is
unchanged.

Framework (tools/adapters/):
- base.py — PluginSource parser, HarnessAdapter ABC, write/mirror helpers
  (path-traversal guard, UTF-8-safe), inline-list + block-list + block-scalar
  YAML-ish parser, _utf8_safe_cut, _split_inline_list, _normalize_author
- capabilities.py — per-harness capability matrix, TOOL_NAME_MAPS,
  MODEL_ALIASES, resolve_model() with explicit warnings
- codex.py — emits .codex/{skills,agents}/ + AGENTS.md (≤150-line
  table-of-contents). Fence-aware body splitter, _utf8_safe_cut for
  multibyte safety, _yaml_scalar with reserved-word + special-char quoting.
  Skill/command name collision detection (and second-order __cmd fallback).
- cursor.py — emits .cursor-plugin/{plugin,marketplace}.json + curated
  .cursor/rules/*.mdc. _validate_mdc_frontmatter handles YAML block scalars
  (no false positives on colons in description body). _normalize_author
  handles dict, npm-style strings, and author lists.
- opencode.py — transpiles agents to .opencode/agents/<id>.md with
  mode:subagent + permission: deny-everything-else block (skill/task always
  allowed as base capabilities — Claude's implicit defaults).
- gemini.py — emits native skills/, agents/, and commands/ at extension
  root (April 2026 spec). Tool-allowlist remapped via TOOL_NAME_MAPS.

CLI + tooling:
- tools/generate.py — unified `make generate HARNESS=<x> [PLUGIN=<y>]`,
  with --clean (containment-guarded; case-insensitive on Darwin/Win32),
  --prune (orphan removal across all per-harness output trees), --strict
  (warnings fail), per-plugin error aggregation, refuses --clean --plugin
  (would silently wipe other plugins' artifacts).
- tools/validate_generated.py — structural validation across all four
  harness outputs. Codex 8KB cap → error. _extract_permission_block
  correctly handles nested permission keys (column-0 only).
- tools/doc_gardener.py — recurring drift detection per OpenAI harness-
  engineering principle. STALE_ARTIFACT (info), DEAD_LINK (error),
  MARKETPLACE_ORPHAN (error), SKILL_OVER_CODEX_CAP (warning), grouped
  output sorted by severity.

plugin-eval (extends existing framework):
- New harness_portability dimension (6% weight, rebalanced from existing
  static sub-scores). Surfaces non-portable patterns with concrete
  remediation hints: SKILL_OVER_CODEX_CAP, CLAUDE_TOOL_REFS,
  CLAUDE_TOOL_PROSE, AGENT_NAME_COLLISION, BARE_MODEL_ALIAS.
- _CAMEL_TOOL_PATTERN requires Claude-tool context (no false positives
  on Rust's `Task` etc.). _TOOL_PROSE_PATTERN case-sensitive on tool
  names, case-insensitive on the leading article.
- Findings do NOT also feed anti_pattern_penalty (no double-counting).

Documentation:
- Top-level guides: CODEX.md, CURSOR.md, OPENCODE.md (≤150 lines each,
  table-of-contents pattern per OpenAI harness-engineering post)
- docs/harnesses.md — capability matrix, graceful-degradation table,
  generated output paths
- docs/authoring.md — portable-content style guide (tools, models,
  collision rules, fence-respect)
- docs/round-trip-results.md — real-CLI verification recipes (OpenCode
  discovers 193 subagents, Gemini extensions validate passes, Codex
  TOMLs all parse)
- CONTRIBUTING.md — new file pointing at docs/authoring.md
- README.md — rewritten for multi-harness (145 lines, was 460)
- CLAUDE.md — trimmed to 60-line table-of-contents
- GEMINI.md — trimmed from 1500 to 500 tokens (3× over budget previously)

Tests: 181 passing (103 plugin-eval + 78 tools/tests). Real-CLI round-trip
verified for OpenCode, Gemini, and Codex (TOML parses).

Replaces tools/generate_gemini_commands.py with the unified CLI.

* refactor(skills): extract detail to references/details.md (~75 skills)

Apply Anthropic's canonical SKILL.md progressive-disclosure pattern across
the marketplace: SKILL.md body becomes a navigation tier (trigger phrasing
+ quick start), detailed templates and worked examples move to
references/details.md (loaded on demand by the agent).

Motivation: OpenAI Codex CLI hard-truncates skills at 8 KB. Before this
change, ~90 skills exceeded that cap and would silently break on Codex.
The progressive-disclosure pattern is also Anthropic's documented
recommendation for token efficiency — Claude Code reads references/ files
on demand when the body navigation says to.

What's extracted, by pattern:
- Pass 1 (## Templates section): 19 skills — full template libraries
  moved to references/details.md
- Pass 2 (## Implementation Patterns / ## Advanced Patterns): 13 skills
- Pass 3 (everything between nav-tier and wrap-tier headings): 53 skills
- Conservative re-extraction for 8 skills that got over-reduced — kept
  ~6-7 KB inline (most of the quick-start tier) plus references/ overflow

What stays inline (SKILL.md navigation tier):
- description: frontmatter (triggering — unchanged for all skills)
- ## When to Use This Skill / ## Core Concepts / ## Quick Start
- ## Best Practices / ## Troubleshooting / ## See Also wrap-ups
- A pointer note ("see references/details.md") so the agent knows where
  to look for detail

What goes to references/details.md (detail tier, on-demand load):
- ## Templates (full code template libraries)
- ## Implementation Patterns / ## Advanced Patterns (deep examples)
- Mid-skill walkthroughs that exceed the inline budget

Also in this commit:
- plugins/brand-landingpage description trimmed from 958→543 chars
  (preserves trigger phrasing, drops verbose example-quote list)

Net effect:
- SKILL_OVER_CODEX_CAP findings: 90 → 10 (88% reduction)
- All triggers unchanged — discovery behavior identical across harnesses
- 75 new references/details.md files with the extracted content
- Same depth of guidance, loaded progressively

Remaining 10 oversized skills are complex multi-section docs (e.g.
postgresql, code-review-excellence, evaluation-methodology) that need
per-skill manual judgment — flagged by `make garden` for future work.

* chore: bump all plugin versions (multi-harness release)

Patch-bump every local plugin (81) in both .claude-plugin/marketplace.json
entries and each plugins/<name>/.claude-plugin/plugin.json. Minor-bump the
top-level marketplace metadata.version (1.6.0 → 1.7.0) to signal the
multi-harness adapter framework addition.

The external git-subdir entry (qa-orchestra) is unaffected — its version
is governed by its upstream repo.

* fix(opencode): preserve explicit tools:[] + word-boundary subtask match

Addresses two Codex review findings on PR #541.

## P1 — `tools: []` silently upgraded to permissive (privilege escalation)

Before: `_build_permission_block` returned `{}` for any empty list, which
omits the `permission:` block entirely from the emitted agent. An author
who explicitly wrote `tools: []` to lock down an advisory-only agent got
an UNRESTRICTED agent in OpenCode. Affected agent in this tree:
`plugins/arm-cortex-microcontrollers/agents/arm-cortex-expert.md`.

Fix: `_build_permission_block` now takes a `has_tools_field` flag so the
caller can distinguish "tools: key missing" (Claude default permissive)
from "tools: []" (explicit lock-down). The lock-down case emits a
deny-everything block that allows ONLY the base capabilities (skill, task)
that Claude Code always grants implicitly. Verified against the real
arm-cortex-expert agent — now emits read/edit/write/bash/grep/glob/list:
deny, task/skill: allow.

## P2 — `"agent" in cmd.body.lower()` false-positives on substrings

Before: a command body containing `PerformanceReviewAgent` (class name
in a code snippet) or `useragent` triggered `subtask: true`, changing
runtime behavior based on incidental text.

Fix: switch to a compiled word-boundary regex `\b(agent|subagent)s?\b`
(case-insensitive). Tests confirm the substring `PerformanceReviewAgent`
no longer fires, while a real "spawn a subagent" sentence still does.

## Tests

3 new regression tests in tools/tests/test_adapters.py:
- `test_explicit_empty_tools_yields_locked_permission_block` (P1)
- `test_missing_tools_field_yields_no_permission_block` (P1 boundary)
- `test_subtask_inference_word_boundary` (P2)

184 total tests pass (was 181). OpenCode round-trip still discovers all
193 subagents; arm-cortex-expert agent is now properly locked down.

* test: behavioral verification + CI gates for multi-harness pipeline

Adds three layers of automated verification that pure-Python parser tests
miss, plus the CI jobs that turn them into hard gates. Catches the kinds
of issues that previously only surfaced when a real user installed the
marketplace and tried to use it.

## test_real_world.py — real-source structural tests

Runs against the actual `plugins/` tree (not synthetic fixtures). Catches
issues that only appear on real content:

- every marketplace entry resolves to a plugins/<name>/ dir
- every local plugin dir appears in marketplace.json
- marketplace.json version == per-plugin plugin.json version (catches drift)
- every plugin loads via load_plugin() without error
- no plugin name contains `__` (adapter namespace separator)
- every agent has name + description; every skill has a trigger phrase
  (same regex plugin_eval's MISSING_TRIGGER check uses)
- no agent name collides with Codex built-ins
- every refactored skill (with `references/details.md`) has:
  - meaningful detail content (>=500 B in details.md)
  - a pointer to references/ in the SKILL.md body
  - a navigation-tier heading preserved (When to Use, Overview, etc.)
  - body >= 600 B (not a stub)
- every plugin.json has name + version matching the dir

This test pass found and fixed three real defects before commit:
- ship-mate/skills/scan: description had no trigger phrase ("Use when…")
- reverse-engineering/skills/memory-forensics: nav-tier section lost
  during extraction
- reverse-engineering/skills/binary-analysis-patterns: same

All three are now fixed (preserved trigger phrasing, added When-to-Use
sections back to the skills my extraction over-trimmed).

## test_round_trip.py — generate→parse→verify

CI runs this AFTER `make generate-all`. Catches generation-time regressions:

- OpenCode/Codex/Gemini agent counts match source agent count (no skips)
- every Codex SKILL.md under 8 KB (the cap that would silently truncate)
- every Codex agent TOML has required fields + valid sandbox_mode
- every OpenCode agent has mode in {primary,subagent,all} and
  provider-prefixed model
- locked agents (source `tools: []`) emit proper deny-everything permission
  block with skill/task allow (regression guard for PR-541 P1)
- every Gemini @{path} injection resolves to a real source file
- every Gemini command TOML has prompt + {{args}} placeholder
- every context file (CLAUDE.md, AGENTS.md, GEMINI.md, etc.) within
  150-line cap
- Cursor marketplace + per-plugin manifests cover all local plugins
- .cursor/rules/*.mdc only use the 3 documented frontmatter keys

## test_cli_smoke.py — real-CLI subprocess tests

Invokes the actual harness binaries (OpenCode, Gemini, Codex, Claude Code)
against the generated artifacts. Catches CLI-level issues pure-Python
parsing can't see: schema-loader drift, plugin-discovery bugs, version
incompatibilities.

- `opencode agent list` — must succeed AND discover every source agent
  (currently 191 + 2 OpenCode built-ins)
- `gemini extensions validate <repo>` — must return success
- `codex doctor` — must report healthy install
- every Codex agent TOML must parse with stdlib `tomllib`
- `claude --version` — sanity check the Claude Code CLI loads
- marketplace.json must have owner + metadata.version for Claude Code's loader

Per-CLI tests skip gracefully when the binary isn't on PATH, so local
devs only exercise what they have installed. CI installs OpenCode +
Gemini and turns those skips into hard gates.

## Makefile + CI

- `make test` — full pytest suite (plugin-eval + tools/tests/)
- `make smoke-test` — generates if needed, then runs real-CLI smoke tests
- `.github/workflows/validate.yml` extended with:
  - `tools-tests` job — runs pytest tools/tests/
  - `multi-harness-generate` job — `make generate-all && make validate
    STRICT=1 && make garden`, uploads generated artifacts on every run
  - `cli-smoke-test` job — installs OpenCode + Gemini, runs test_cli_smoke.py

## Test counts

- Before: 184 tests
- After: 386 tests (parameterized real-source tests over all 82 plugins)
- All passing locally on OpenCode 1.15.7 + Gemini 0.42.0 + Codex 0.133.0
  + Claude Code 2.1.148
2026-05-22 08:18:21 -04:00

11 KiB

rag-implementation — detailed patterns and worked examples

Advanced RAG Patterns

Pattern 1: Hybrid Search with RRF

from langchain_community.retrievers import BM25Retriever
from langchain.retrievers import EnsembleRetriever

# Sparse retriever (BM25 for keyword matching)
bm25_retriever = BM25Retriever.from_documents(documents)
bm25_retriever.k = 10

# Dense retriever (embeddings for semantic search)
dense_retriever = vectorstore.as_retriever(search_kwargs={"k": 10})

# Combine with Reciprocal Rank Fusion weights
ensemble_retriever = EnsembleRetriever(
    retrievers=[bm25_retriever, dense_retriever],
    weights=[0.3, 0.7]  # 30% keyword, 70% semantic
)

Pattern 2: Multi-Query Retrieval

from langchain.retrievers.multi_query import MultiQueryRetriever

# Generate multiple query perspectives for better recall
multi_query_retriever = MultiQueryRetriever.from_llm(
    retriever=vectorstore.as_retriever(search_kwargs={"k": 5}),
    llm=llm
)

# Single query → multiple variations → combined results
results = await multi_query_retriever.ainvoke("What is the main topic?")

Pattern 3: Contextual Compression

from langchain.retrievers import ContextualCompressionRetriever
from langchain.retrievers.document_compressors import LLMChainExtractor

# Compressor extracts only relevant portions
compressor = LLMChainExtractor.from_llm(llm)

compression_retriever = ContextualCompressionRetriever(
    base_compressor=compressor,
    base_retriever=vectorstore.as_retriever(search_kwargs={"k": 10})
)

# Returns only relevant parts of documents
compressed_docs = await compression_retriever.ainvoke("specific query")

Pattern 4: Parent Document Retriever

from langchain.retrievers import ParentDocumentRetriever
from langchain.storage import InMemoryStore
from langchain_text_splitters import RecursiveCharacterTextSplitter

# Small chunks for precise retrieval, large chunks for context
child_splitter = RecursiveCharacterTextSplitter(chunk_size=400, chunk_overlap=50)
parent_splitter = RecursiveCharacterTextSplitter(chunk_size=2000, chunk_overlap=200)

# Store for parent documents
docstore = InMemoryStore()

parent_retriever = ParentDocumentRetriever(
    vectorstore=vectorstore,
    docstore=docstore,
    child_splitter=child_splitter,
    parent_splitter=parent_splitter
)

# Add documents (splits children, stores parents)
await parent_retriever.aadd_documents(documents)

# Retrieval returns parent documents with full context
results = await parent_retriever.ainvoke("query")

Pattern 5: HyDE (Hypothetical Document Embeddings)

from langchain_core.prompts import ChatPromptTemplate

class HyDEState(TypedDict):
    question: str
    hypothetical_doc: str
    context: list[Document]
    answer: str

hyde_prompt = ChatPromptTemplate.from_template(
    """Write a detailed passage that would answer this question:

    Question: {question}

    Passage:"""
)

async def generate_hypothetical(state: HyDEState) -> HyDEState:
    """Generate hypothetical document for better retrieval."""
    messages = hyde_prompt.format_messages(question=state["question"])
    response = await llm.ainvoke(messages)
    return {"hypothetical_doc": response.content}

async def retrieve_with_hyde(state: HyDEState) -> HyDEState:
    """Retrieve using hypothetical document."""
    # Use hypothetical doc for retrieval instead of original query
    docs = await retriever.ainvoke(state["hypothetical_doc"])
    return {"context": docs}

# Build HyDE RAG graph
builder = StateGraph(HyDEState)
builder.add_node("hypothetical", generate_hypothetical)
builder.add_node("retrieve", retrieve_with_hyde)
builder.add_node("generate", generate)
builder.add_edge(START, "hypothetical")
builder.add_edge("hypothetical", "retrieve")
builder.add_edge("retrieve", "generate")
builder.add_edge("generate", END)

hyde_rag = builder.compile()

Document Chunking Strategies

Recursive Character Text Splitter

from langchain_text_splitters import RecursiveCharacterTextSplitter

splitter = RecursiveCharacterTextSplitter(
    chunk_size=1000,
    chunk_overlap=200,
    length_function=len,
    separators=["\n\n", "\n", ". ", " ", ""]  # Try in order
)

chunks = splitter.split_documents(documents)

Token-Based Splitting

from langchain_text_splitters import TokenTextSplitter

splitter = TokenTextSplitter(
    chunk_size=512,
    chunk_overlap=50,
    encoding_name="cl100k_base"  # OpenAI tiktoken encoding
)

Semantic Chunking

from langchain_experimental.text_splitter import SemanticChunker

splitter = SemanticChunker(
    embeddings=embeddings,
    breakpoint_threshold_type="percentile",
    breakpoint_threshold_amount=95
)

Markdown Header Splitter

from langchain_text_splitters import MarkdownHeaderTextSplitter

headers_to_split_on = [
    ("#", "Header 1"),
    ("##", "Header 2"),
    ("###", "Header 3"),
]

splitter = MarkdownHeaderTextSplitter(
    headers_to_split_on=headers_to_split_on,
    strip_headers=False
)

Vector Store Configurations

Pinecone (Serverless)

from pinecone import Pinecone, ServerlessSpec
from langchain_pinecone import PineconeVectorStore

# Initialize Pinecone client
pc = Pinecone(api_key=os.environ["PINECONE_API_KEY"])

# Create index if needed
if "my-index" not in pc.list_indexes().names():
    pc.create_index(
        name="my-index",
        dimension=1024,  # voyage-3-large dimensions
        metric="cosine",
        spec=ServerlessSpec(cloud="aws", region="us-east-1")
    )

# Create vector store
index = pc.Index("my-index")
vectorstore = PineconeVectorStore(index=index, embedding=embeddings)

Weaviate

import weaviate
from langchain_weaviate import WeaviateVectorStore

client = weaviate.connect_to_local()  # or connect_to_weaviate_cloud()

vectorstore = WeaviateVectorStore(
    client=client,
    index_name="Documents",
    text_key="content",
    embedding=embeddings
)

Chroma (Local Development)

from langchain_chroma import Chroma

vectorstore = Chroma(
    collection_name="my_collection",
    embedding_function=embeddings,
    persist_directory="./chroma_db"
)

pgvector (PostgreSQL)

from langchain_postgres.vectorstores import PGVector

connection_string = "postgresql+psycopg://user:pass@localhost:5432/vectordb"

vectorstore = PGVector(
    embeddings=embeddings,
    collection_name="documents",
    connection=connection_string,
)

Retrieval Optimization

1. Metadata Filtering

from langchain_core.documents import Document

# Add metadata during indexing
docs_with_metadata = []
for doc in documents:
    doc.metadata.update({
        "source": doc.metadata.get("source", "unknown"),
        "category": determine_category(doc.page_content),
        "date": datetime.now().isoformat()
    })
    docs_with_metadata.append(doc)

# Filter during retrieval
results = await vectorstore.asimilarity_search(
    "query",
    filter={"category": "technical"},
    k=5
)

2. Maximal Marginal Relevance (MMR)

# Balance relevance with diversity
results = await vectorstore.amax_marginal_relevance_search(
    "query",
    k=5,
    fetch_k=20,  # Fetch 20, return top 5 diverse
    lambda_mult=0.5  # 0=max diversity, 1=max relevance
)

3. Reranking with Cross-Encoder

from sentence_transformers import CrossEncoder

reranker = CrossEncoder('cross-encoder/ms-marco-MiniLM-L-6-v2')

async def retrieve_and_rerank(query: str, k: int = 5) -> list[Document]:
    # Get initial results
    candidates = await vectorstore.asimilarity_search(query, k=20)

    # Rerank
    pairs = [[query, doc.page_content] for doc in candidates]
    scores = reranker.predict(pairs)

    # Sort by score and take top k
    ranked = sorted(zip(candidates, scores), key=lambda x: x[1], reverse=True)
    return [doc for doc, score in ranked[:k]]

4. Cohere Rerank

from langchain.retrievers import CohereRerank
from langchain_cohere import CohereRerank

reranker = CohereRerank(model="rerank-english-v3.0", top_n=5)

# Wrap retriever with reranking
reranked_retriever = ContextualCompressionRetriever(
    base_compressor=reranker,
    base_retriever=vectorstore.as_retriever(search_kwargs={"k": 20})
)

Prompt Engineering for RAG

Contextual Prompt with Citations

rag_prompt = ChatPromptTemplate.from_template(
    """Answer the question based on the context below. Include citations using [1], [2], etc.

    If you cannot answer based on the context, say "I don't have enough information."

    Context:
    {context}

    Question: {question}

    Instructions:
    1. Use only information from the context
    2. Cite sources with [1], [2] format
    3. If uncertain, express uncertainty

    Answer (with citations):"""
)

Structured Output for RAG

from pydantic import BaseModel, Field

class RAGResponse(BaseModel):
    answer: str = Field(description="The answer based on context")
    confidence: float = Field(description="Confidence score 0-1")
    sources: list[str] = Field(description="Source document IDs used")
    reasoning: str = Field(description="Brief reasoning for the answer")

# Use with structured output
structured_llm = llm.with_structured_output(RAGResponse)

Evaluation Metrics

from typing import TypedDict

class RAGEvalMetrics(TypedDict):
    retrieval_precision: float  # Relevant docs / retrieved docs
    retrieval_recall: float     # Retrieved relevant / total relevant
    answer_relevance: float     # Answer addresses question
    faithfulness: float         # Answer grounded in context
    context_relevance: float    # Context relevant to question

async def evaluate_rag_system(
    rag_chain,
    test_cases: list[dict]
) -> RAGEvalMetrics:
    """Evaluate RAG system on test cases."""
    metrics = {k: [] for k in RAGEvalMetrics.__annotations__}

    for test in test_cases:
        result = await rag_chain.ainvoke({"question": test["question"]})

        # Retrieval metrics
        retrieved_ids = {doc.metadata["id"] for doc in result["context"]}
        relevant_ids = set(test["relevant_doc_ids"])

        precision = len(retrieved_ids & relevant_ids) / len(retrieved_ids)
        recall = len(retrieved_ids & relevant_ids) / len(relevant_ids)

        metrics["retrieval_precision"].append(precision)
        metrics["retrieval_recall"].append(recall)

        # Use LLM-as-judge for quality metrics
        quality = await evaluate_answer_quality(
            question=test["question"],
            answer=result["answer"],
            context=result["context"],
            expected=test.get("expected_answer")
        )
        metrics["answer_relevance"].append(quality["relevance"])
        metrics["faithfulness"].append(quality["faithfulness"])
        metrics["context_relevance"].append(quality["context_relevance"])

    return {k: sum(v) / len(v) for k, v in metrics.items()}