publish-manifest.txt

# Deep-research plugin publish manifest
# Source: ~/.claude/plugins/coordinator-claude/deep-research/
# Target: X:/deep-research-claude/
#
# Manifest mode: selective copy, no delete. Target has extra files
# (README.md, LICENSE, docs/) that don't exist in source.

# Staleness scan: SCAN: <subdir> directives walk that source subdir on every
# /percolate run and warn for any file not listed in the manifest below. Without
# them, drift goes silent (proven by the May 2026 driver-file gap — three
# load-bearing pipeline files lived in source for ~10 days while the manifest
# claimed coverage). Add new subdirs here as the plugin grows.
SCAN: agents
SCAN: commands
SCAN: pipelines
SCAN: skills
SCAN: notebooklm
SCAN: .claude-plugin
SCAN: scripts
SCAN: docs/install

# Config
CLAUDE.md

# Top-level plugin manifest — source-authoritative (F4, 2026-06-08).
# Bump version + repository URL in source; percolate ships the change.
.claude-plugin/plugin.json

# Agent definitions
agents/coverage-auditor.md
agents/repo-scout.md
agents/repo-specialist.md
agents/research-scout.md
agents/research-specialist.md
agents/research-synthesizer.md
agents/structured-synthesizer.md

# Commands
# (repo.md, structured.md, web.md collapsed into research.md --mode in v1.3.0)
commands/research.md
commands/install.md

# Cleanup from rename (2026-06-15): /deep-research:setup -> /deep-research:install
DELETE: commands/setup.md

# Pipelines
pipelines/PIPELINE.md
pipelines/coverage-auditor-prompt-template.md
pipelines/spec-format.md
pipelines/eval-rubric.md
pipelines/gap-specialist-prompt-template.md
pipelines/repo-atlas-prompt-template.md
pipelines/repo-atlas-sketch-prompt-template.md
pipelines/repo-driver.md
pipelines/repo-research-internals.md
pipelines/repo-scout-prompt-template.md
pipelines/repo-specialist-prompt-template.md
pipelines/repo-survey-prompt-template.md
pipelines/repo-synthesizer-prompt-template.md
pipelines/repo-team-protocol.md
pipelines/scout-prompt-template.md
pipelines/specialist-prompt-template.md
pipelines/structured-driver.md
pipelines/structured-scout-prompt-template.md
pipelines/structured-synthesizer-prompt-template.md
pipelines/structured-team-protocol.md
pipelines/structured-verifier-prompt-template.md
pipelines/team-protocol.md
pipelines/web-driver.md
pipelines/web-research-internals.md

# Skills
skills/eval-output.md
skills/setup/SKILL.md

# Install-chain contract (chain step 4 of 5 — leaf-bootstrap walkable).
# The agent-install-manifest declares standalone_setup_script: scripts/setup.{sh,ps1};
# these resolve at the flat publish-repo root (no layout transform — DR publishes flat,
# unlike coordinator which nests under coordinator/). The chain-walker sources scripts/lib/*.
# Added 2026-06-17 to land the manifest pair on the OSS mirror (the gap project-rag-em flagged).
docs/install/agent-install-manifest.json
docs/install/agent-install-manifest.schema.json
docs/install/AGENT.md
scripts/setup.sh
scripts/setup.ps1
scripts/lib/chain_walker_subagent_prompt.txt
scripts/lib/dep_check.ps1
scripts/lib/dep_check.sh
scripts/lib/dep_consent_banner.txt
scripts/lib/dr_capability_probe.sh
scripts/lib/manifest_reader.ps1
# Prereq probe unit vendored from coordinator (byte-identical SSOT); setup.sh sources
# manifest_reader.sh + prereq_probe.sh from coordinator_prereq/, prereq_probe self-sources
# step_zero_emit.sh from the same isolated dir (nested-layout, 2026-06-23 reorg).
scripts/lib/coordinator_prereq/manifest_reader.sh
scripts/lib/coordinator_prereq/prereq_probe.sh
scripts/lib/coordinator_prereq/step_zero_emit.sh

# NotebookLM (Pipeline D)
notebooklm/CLAUDE.md
notebooklm/.claude-plugin/plugin.json
notebooklm/.mcp.json
notebooklm/agents/notebooklm-research-scout.md
notebooklm/agents/research-sweep.md
notebooklm/agents/research-worker.md
notebooklm/commands/notebooklm-research.md
notebooklm/pipelines/team-protocol.md
notebooklm/pipelines/scout-prompt-template.md
notebooklm/pipelines/sweep-prompt-template.md
notebooklm/pipelines/worker-prompt-template.md
notebooklm/pipelines/notebooklm-best-practices.md