v1.0.0: feature-complete initial release

Author: drader

.claude-plugin/plugin.json

@@ -0,0 +1,43 @@
+{
+  "name": "researcher_agent",
+  "version": "1.0.0",
+  "description": "LLM-driven research assistance framework: end-to-end pipeline from research question through manuscript delivery. 4 skills (research, compose, critique, orchestrate), 24 modes, 24 slash commands. Human-in-the-loop with mandatory checkpoints. CC BY-NC 4.0.",
+  "author": {
+    "name": "Oğuz Gençer",
+    "year": 2026
+  },
+  "license": "CC-BY-NC-4.0",
+  "license_file": "LICENSE",
+  "homepage": "https://github.com/oguzgencer/researcher_agent",
+  "skills": [
+    {
+      "name": "research",
+      "path": "skills/research",
+      "description": "Literature investigation, source verification, synthesis. 7 modes: brief, full, socratic, systematic, verify, annotate, evaluate."
+    },
+    {
+      "name": "compose",
+      "path": "skills/compose",
+      "description": "Manuscript drafting, revision, formatting. 9 modes: full, outline, revision, revision-triage, abstract, lit-section, format, citation-check, disclosure."
+    },
+    {
+      "name": "critique",
+      "path": "skills/critique",
+      "description": "Peer-review-style manuscript critique (simulation, not substitute). 6 modes: full, quick, methodology, re-review, guided, calibration."
+    },
+    {
+      "name": "orchestrate",
+      "path": "skills/orchestrate",
+      "description": "End-to-end pipeline orchestrator. Sequences research, compose, and critique skills across a 10-stage workflow with mandatory checkpoints. 2 modes: pipeline, resume."
+    }
+  ],
+  "commands_dir": "commands",
+  "agents_dir": "agents",
+  "phase": "4 of 4 (feature-complete)",
+  "phases_released": {
+    "1": "research (v0.1.0)",
+    "2": "compose (v0.2.0)",
+    "3": "critique (v0.3.0)",
+    "4": "orchestrate (v1.0.0)"
+  }
+}

.github/ISSUE_TEMPLATE/bug-report.yml

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+name: 🐛 Bug report
+description: Something doesn't work as the framework promises
+title: "[bug]: "
+labels: ["bug", "triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to file a bug report.
+        Before submitting, please check:
+        - If this is a **security vulnerability**, use [private reporting](https://github.com/drader/researcher_agent/security/advisories/new) instead. See [SECURITY.md](https://github.com/drader/researcher_agent/blob/main/SECURITY.md) for scope.
+        - If this is a **source-grounding failure** (fabricated citation, undisclosed AI use, provenance break), please use that template instead — those have framework-specific implications.
+        - If this is a **question** rather than a bug, please open a [Discussion](https://github.com/drader/researcher_agent/discussions).
+
+  - type: textarea
+    id: summary
+    attributes:
+      label: Summary
+      description: One or two sentences. What did you expect, what happened instead?
+      placeholder: "I invoked /research-systematic with X and expected Y, but got Z."
+    validations:
+      required: true
+
+  - type: textarea
+    id: repro
+    attributes:
+      label: Reproduction steps
+      description: |
+        Minimum command(s) or input(s) needed to reproduce.
+        Please include the exact slash command, mode, and any text the framework was asked to operate on (paraphrase if confidential).
+      placeholder: |
+        1. Run `/research-verify` on the attached paragraph
+        2. Observe the verdict for claim 3
+        3. ...
+      render: markdown
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected behaviour
+      description: Cite the stated guarantee if possible (ARCHITECTURE.md, the relevant SKILL.md, or a Principle).
+    validations:
+      required: true
+
+  - type: textarea
+    id: actual
+    attributes:
+      label: Observed behaviour
+      description: What actually happened. Verbatim output is most useful.
+    validations:
+      required: true
+
+  - type: input
+    id: framework-version
+    attributes:
+      label: researcher_agent version
+      description: From `CHANGELOG.md` or the README status section.
+      placeholder: "v1.0.0"
+    validations:
+      required: true
+
+  - type: input
+    id: model
+    attributes:
+      label: Claude model identifier (if relevant)
+      description: Helpful when the bug depends on the underlying model.
+      placeholder: "e.g. claude-sonnet-4-6"
+
+  - type: textarea
+    id: additional
+    attributes:
+      label: Additional context
+      description: Logs, `pipeline-logbook.json` excerpts, screenshots — anything else that helps.

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: 🔒 Security vulnerability
+    url: https://github.com/drader/researcher_agent/security/advisories/new
+    about: |
+      Please do not open a public Issue for a security report.
+      Use GitHub's private vulnerability reporting. See SECURITY.md for scope and what to expect.
+  - name: 💬 Question or open discussion
+    url: https://github.com/drader/researcher_agent/discussions
+    about: |
+      For questions, design discussions, "how would I…" prompts, or anything that isn't a concrete bug,
+      proposal, source-grounding failure, or documentation issue, open a Discussion instead.

.github/ISSUE_TEMPLATE/documentation-issue.yml

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+name: 📖 Documentation issue
+description: A documented claim is wrong, unclear, missing, or out of date
+title: "[docs]: "
+labels: ["documentation"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for flagging this.
+
+        Before submitting, please check whether the issue is **drift between dependent documents**
+        (where one file disagrees with the authoritative source). If yes, the "Single sources of truth"
+        table in [CLAUDE.md](https://github.com/drader/researcher_agent/blob/main/CLAUDE.md) tells you which
+        file should win — the fix is to update the dependent, not the authority.
+
+  - type: dropdown
+    id: nature
+    attributes:
+      label: Nature of the issue
+      options:
+        - Incorrect / inaccurate
+        - Unclear / ambiguous
+        - Out of date (drift from current behaviour)
+        - Missing (something is not documented but should be)
+        - Inconsistent across files
+      default: 0
+    validations:
+      required: true
+
+  - type: input
+    id: file
+    attributes:
+      label: File path
+      description: The primary file affected. Use a repo-relative path.
+      placeholder: "e.g. ARCHITECTURE.md, skills/research/SKILL.md, index.html"
+    validations:
+      required: true
+
+  - type: input
+    id: section
+    attributes:
+      label: Section or line
+      description: |
+        Section heading, line range, or slide number. Helps reviewers find the spot.
+      placeholder: "§ Provenance, or slide 14, or lines 60-72"
+
+  - type: textarea
+    id: what-it-says
+    attributes:
+      label: What the document currently says
+      description: Quote the relevant passage verbatim.
+    validations:
+      required: true
+
+  - type: textarea
+    id: what-it-should-say
+    attributes:
+      label: What it should say (and why)
+      description: |
+        Proposed wording or correction.
+        If the issue is inconsistency with another file, name the other file and which one you believe is authoritative per CLAUDE.md.
+    validations:
+      required: true
+
+  - type: checkboxes
+    id: parity-impact
+    attributes:
+      label: Parity impact (per CLAUDE.md)
+      description: If accepted, would this also require updating any of the following?
+      options:
+        - label: index.html
+        - label: architecture.html
+        - label: docs/diagrams/*.svg
+        - label: CITATION.cff
+        - label: CHANGELOG.md (counts as a change)
+        - label: One of the registries (MODE_REGISTRY, AGENT_REGISTRY)

.github/ISSUE_TEMPLATE/mode-or-skill-proposal.yml

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+name: ✨ Mode or skill proposal
+description: Propose a new mode, new skill, or new sub-agent persona
+title: "[proposal]: "
+labels: ["proposal", "discussion"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for thinking about how to extend the framework.
+        Before submitting, please skim [POSITIONING.md](https://github.com/drader/researcher_agent/blob/main/POSITIONING.md) for what's in scope, and [CONTRIBUTING.md](https://github.com/drader/researcher_agent/blob/main/CONTRIBUTING.md) for the contribution flow.
+
+        For open-ended ideas that aren't ready for a concrete proposal, a [Discussion](https://github.com/drader/researcher_agent/discussions) is the better starting place.
+
+  - type: dropdown
+    id: type
+    attributes:
+      label: Type of proposal
+      description: What are you proposing to add?
+      options:
+        - New mode in an existing skill
+        - New skill
+        - New sub-agent persona
+        - New slash command (variant of an existing mode)
+      default: 0
+    validations:
+      required: true
+
+  - type: input
+    id: name
+    attributes:
+      label: Proposed name
+      description: Use kebab-case. For modes, follow the existing naming.
+      placeholder: "e.g. critique-replication or research-meta-analysis"
+    validations:
+      required: true
+
+  - type: input
+    id: parent
+    attributes:
+      label: Parent skill (if applicable)
+      description: For modes and personas. Leave blank if proposing a new skill.
+      placeholder: "e.g. research"
+
+  - type: dropdown
+    id: spectrum
+    attributes:
+      label: Spectrum bias (for modes)
+      description: Where does this mode sit on the Generative ↔ Hybrid ↔ Analytic spectrum?
+      options:
+        - Generative
+        - Hybrid
+        - Analytic
+        - Not applicable (not a mode)
+
+  - type: textarea
+    id: gap
+    attributes:
+      label: What gap does this fill?
+      description: |
+        Be concrete. Describe a real workflow this would unlock.
+        If an existing mode/skill/persona almost does this, explain why "almost" isn't enough.
+    validations:
+      required: true
+
+  - type: textarea
+    id: role
+    attributes:
+      label: Proposed role / deliverable
+      description: |
+        For a mode: the deliverable it produces and its oversight level.
+        For a skill: the workflows it owns.
+        For a persona: the single role-boundary description.
+    validations:
+      required: true
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives considered
+      description: |
+        Existing modes/skills/personas you considered and discarded.
+        "Just use mode X" is the most common response to a proposal; address it preemptively.
+
+  - type: checkboxes
+    id: registry-impact
+    attributes:
+      label: Registry impact (per CLAUDE.md)
+      description: What canonical files would the implementation need to update?
+      options:
+        - label: MODE_REGISTRY.md
+        - label: AGENT_REGISTRY.md
+        - label: ARCHITECTURE.md
+        - label: README.md + HTML report pages
+        - label: SKILL.md of the parent skill