specsmith 0.11.3.dev432__tar.gz → 0.11.3.dev435__tar.gz

{specsmith-0.11.3.dev432/src/specsmith.egg-info → specsmith-0.11.3.dev435}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: specsmith
-Version: 0.11.3.dev432
+Version: 0.11.3.dev435
 Summary: Applied Epistemic Engineering toolkit — AEE agent sessions, execution profiles, FPGA/HDL governance, tool installer, 50+ CLI commands.
 Author: BitConcepts
 License-Expression: MIT

{specsmith-0.11.3.dev432 → specsmith-0.11.3.dev435}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "specsmith"
-version = "0.11.3.dev432"
+version = "0.11.3.dev435"
 description = "Applied Epistemic Engineering toolkit — AEE agent sessions, execution profiles, FPGA/HDL governance, tool installer, 50+ CLI commands."
 readme = "README.md"
 license = "MIT"

{specsmith-0.11.3.dev432 → specsmith-0.11.3.dev435}/src/specsmith/config.py

@@ -66,6 +66,8 @@ class ProjectType(str, Enum):
     EMBEDDED_PYTHON_HMI = "embedded-python-hmi"  # #109: hardware-interfacing kiosk/HMI
     RESEARCH_PYTHON = "research-python"  # #153: experiment/research packages (no CLI)
     SAFETY_CRITICAL = "safety-critical"  # #129: IEC 60204-1/62061/61508 safety-critical
+    # IP / Patent
+    PATENT_PROSECUTION = "patent-prosecution"  # #177: IP prosecution with USPTO MCP lifecycle
 
 
 class Platform(str, Enum):
@@ -194,6 +196,67 @@ class ProjectConfig(BaseModel):
         ),
     )
 
+    # Fallback type — used when this project type is not yet supported
+    # by the installed specsmith version. specsmith silently falls back to
+    # this type for scaffolding purposes while still recording the intended type.
+    fallback_type: str = Field(
+        default="",
+        description=(
+            "Fallback project type for scaffold generation when `type` is not yet "
+            "supported by the installed specsmith version (e.g. 'spec-document' as "
+            "fallback for 'patent-prosecution')."
+        ),
+    )
+
+    # IP prosecution fields (used when type == 'patent-prosecution')
+    provisional_app_number: str = Field(
+        default="", description="USPTO provisional application number (e.g. '63/980,251')"
+    )
+    provisional_filed_date: str = Field(
+        default="", description="Date the provisional was filed (YYYY-MM-DD)"
+    )
+    non_provisional_deadline: str = Field(
+        default="",
+        description="12-month non-provisional conversion deadline (YYYY-MM-DD)",
+    )
+    entity_status: str = Field(default="", description="USPTO entity status: small, micro, large")
+    assignee: str = Field(default="", description="Patent assignee / rights holder")
+    counsel: str = Field(default="", description="Patent counsel firm name")
+    inventors: list[dict[str, str]] = Field(
+        default_factory=list,
+        description="List of inventors with name and role keys",
+    )
+    ip_families: list[dict[str, Any]] = Field(
+        default_factory=list,
+        description=(
+            "IP patent families. Each entry: {id, name, phase, provisional, themes, "
+            "anchor_spec, ...}."
+        ),
+    )
+    claim_themes: list[dict[str, Any]] = Field(
+        default_factory=list,
+        description=(
+            "Claim themes for the primary IP family. Each entry: {id, name, description, "
+            "risk, primary_comparator, last_par_run}."
+        ),
+    )
+    specs_dir: str = Field(
+        default="docs/ip/specs",
+        description="Normative specification directory for IP repos",
+    )
+    prosecution_dir: str = Field(
+        default="docs/ip/prosecution",
+        description="Prior-art protocol and prosecution planning directory",
+    )
+    strategy_dir: str = Field(
+        default="docs/ip/strategy",
+        description="IP strategy documents directory",
+    )
+    filings_dir: str = Field(
+        default="docs/ip/filings",
+        description="Immutable filed artifacts directory",
+    )
+
     # FPGA-specific
     fpga_vendor: str = Field(
         default="",
@@ -471,6 +534,8 @@ _TYPE_LABELS: dict[str, str] = {
     ProjectType.EMBEDDED_PYTHON_HMI: "Embedded Python HMI / kiosk (hardware-interfacing)",
     ProjectType.RESEARCH_PYTHON: "Research Python (experiments, no CLI distribution)",
     ProjectType.SAFETY_CRITICAL: "Safety-critical embedded (IEC 60204-1/62061/61508)",
+    # IP / Patent
+    ProjectType.PATENT_PROSECUTION: "Patent prosecution repository (USPTO IP lifecycle)",
 }
 
 _SECTION_REFS: dict[str, str] = {

{specsmith-0.11.3.dev432 → specsmith-0.11.3.dev435}/src/specsmith/phase.py

@@ -398,6 +398,153 @@ PHASES: list[Phase] = [
 PHASE_MAP: dict[str, Phase] = {p.key: p for p in PHASES}
 PHASE_ORDER: list[str] = [p.key for p in PHASES]
 
+# ---------------------------------------------------------------------------
+# IP Prosecution phases  (patent-prosecution project type — issue #177)
+# ---------------------------------------------------------------------------
+
+PROSECUTION_PHASES: list[Phase] = [
+    Phase(
+        key="provisional-draft",
+        label="Provisional Draft",
+        emoji="\U0001f4dd",
+        description="Invention disclosure and provisional specification being written.",
+        checks=[
+            PhaseCheck("AGENTS.md exists", _file_exists("AGENTS.md")),
+            PhaseCheck("docs/ip/specs/ exists", _file_exists("docs/ip/specs")),
+            PhaseCheck("scaffold.yml has ip_families field", _scaffold_field("ip_families")),
+        ],
+        commands=["specsmith audit", 'specsmith ledger add "Provisional draft in progress"'],
+        next_phase="filing",
+    ),
+    Phase(
+        key="filing",
+        label="Filing",
+        emoji="\U0001f4e8",
+        description="Provisional application prepared and submitted to USPTO.",
+        checks=[
+            PhaseCheck("docs/ip/filings/ exists", _file_exists("docs/ip/filings")),
+            PhaseCheck(
+                "scaffold.yml has provisional_app_number",
+                _scaffold_field("provisional_app_number"),
+            ),
+            PhaseCheck(
+                "scaffold.yml has provisional_filed_date",
+                _scaffold_field("provisional_filed_date"),
+            ),
+        ],
+        commands=[
+            'specsmith ledger add "Provisional filed at USPTO — App. <number>"',
+            'specsmith trace seal milestone "Provisional filed"',
+        ],
+        next_phase="prior-art-search",
+    ),
+    Phase(
+        key="prior-art-search",
+        label="Prior-Art Search",
+        emoji="\U0001f50e",
+        description="Systematic prior-art protocol executed across all claim themes.",
+        checks=[
+            PhaseCheck(
+                "scaffold.yml has provisional_app_number",
+                _scaffold_field("provisional_app_number"),
+            ),
+            PhaseCheck(
+                "LEDGER.md has PAR run entry",
+                lambda root: any(
+                    "PAR-" in (root / c).read_text(encoding="utf-8", errors="ignore")
+                    for c in ["docs/LEDGER.md", "LEDGER.md"]
+                    if (root / c).exists()
+                ),
+            ),
+            PhaseCheck("docs/ip/prosecution/ exists", _file_exists("docs/ip/prosecution")),
+        ],
+        commands=[
+            "prior-art protocol: start Themes A-H (USPTO MCP)",
+            'specsmith ledger add "PAR-YYYY-MM-DD-001 complete — Themes A-H"',
+        ],
+        next_phase="claim-hardening",
+    ),
+    Phase(
+        key="claim-hardening",
+        label="Claim Hardening",
+        emoji="\U0001f527",
+        description="Claim language refined based on prior-art findings; §101/§102/§103 addressed.",
+        checks=[
+            PhaseCheck(
+                "LEDGER.md has PAR run entry",
+                lambda root: any(
+                    "PAR-" in (root / c).read_text(encoding="utf-8", errors="ignore")
+                    for c in ["docs/LEDGER.md", "LEDGER.md"]
+                    if (root / c).exists()
+                ),
+            ),
+            PhaseCheck("docs/ip/specs/ has content", _file_min_lines("docs/ip/specs", 1)),
+            PhaseCheck("docs/ip/strategy/ exists", _file_exists("docs/ip/strategy")),
+        ],
+        commands=[
+            'specsmith ledger add "Claim hardening session — Theme <X> hardened"',
+            'specsmith trace seal decision "Claim strategy approved by counsel"',
+        ],
+        next_phase="non-provisional-draft",
+    ),
+    Phase(
+        key="non-provisional-draft",
+        label="Non-Provisional Draft",
+        emoji="\U0001f4c4",
+        description="Anchor non-provisional and continuation drafts being prepared by counsel.",
+        checks=[
+            PhaseCheck(
+                "scaffold.yml has non_provisional_deadline",
+                _scaffold_field("non_provisional_deadline"),
+            ),
+            PhaseCheck("docs/ip/filings/ exists", _file_exists("docs/ip/filings")),
+            PhaseCheck("docs/ip/strategy/ exists", _file_exists("docs/ip/strategy")),
+        ],
+        commands=[
+            'specsmith ledger add "Non-provisional draft v<N> submitted to counsel"',
+        ],
+        next_phase="examination",
+    ),
+    Phase(
+        key="examination",
+        label="Examination",
+        emoji="\U0001f50d",
+        description="Application under examination at USPTO. Responding to office actions.",
+        checks=[
+            PhaseCheck("docs/ip/filings/ exists", _file_exists("docs/ip/filings")),
+            PhaseCheck(
+                "scaffold.yml has provisional_app_number",
+                _scaffold_field("provisional_app_number"),
+            ),
+        ],
+        commands=[
+            'specsmith ledger add "OA response filed — <date>"',
+            'specsmith trace seal milestone "Office action response submitted"',
+        ],
+        next_phase="allowance",
+    ),
+    Phase(
+        key="allowance",
+        label="Allowance",
+        emoji="\u2705",
+        description="Patent allowed or continuation strategy in execution.",
+        checks=[
+            PhaseCheck("docs/ip/filings/ exists", _file_exists("docs/ip/filings")),
+            PhaseCheck("Trace vault has seals", _trace_vault_exists()),
+        ],
+        commands=[
+            'specsmith ledger add "NOA received — patent allowed"',
+            'specsmith trace seal milestone "Patent allowed"',
+        ],
+        next_phase=None,
+    ),
+]
+
+# Merge prosecution phases into PHASE_MAP so read_phase() can find them.
+# Prosecution phases are intentionally NOT in PHASE_ORDER (the AEE sequence).
+PROSECUTION_PHASE_MAP: dict[str, Phase] = {p.key: p for p in PROSECUTION_PHASES}
+PHASE_MAP.update(PROSECUTION_PHASE_MAP)
+
 
 # ---------------------------------------------------------------------------
 # scaffold.yml I/O

{specsmith-0.11.3.dev432 → specsmith-0.11.3.dev435}/src/specsmith/skills/devops.py

@@ -4,6 +4,192 @@
 from specsmith.skills import SkillDomain, SkillEntry
 
 SKILLS: list[SkillEntry] = [
+    SkillEntry(
+        slug="github-health-check",
+        name="GitHub Health Check — CI/PR/security/code-quality triage",
+        description=(
+            "Systematic triage playbook for GitHub repository health: CI failures, "
+            "open PRs and review status, CodeQL security alerts, Dependabot alerts, "
+            "and code quality issues. Uses gh CLI and gh api exclusively."
+        ),
+        domain=SkillDomain.DEVOPS,
+        tags=[
+            "ci",
+            "github",
+            "security",
+            "codeql",
+            "dependabot",
+            "pr",
+            "triage",
+            "alerts",
+            "code-quality",
+            "gh",
+        ],
+        platforms=["linux", "windows", "macos"],
+        prerequisites=["gh"],
+        body="""\
+# GitHub Health Check Skill
+
+## Triage order (always run in this sequence)
+1. **CI status** — are the latest runs passing?
+2. **Open PRs** — any blocked, unreviewed, or failing PRs?
+3. **CodeQL / security alerts** — any open code-scanning alerts?
+4. **Dependabot alerts** — any vulnerable dependencies?
+5. **Code quality / policy violations** — any rule violations?
+
+---
+
+## 1. CI status
+```bash
+# Latest runs on a branch (all workflows)
+gh run list --repo <owner>/<repo> --branch <branch> --limit 5
+
+# Check conclusion of the single latest run
+gh run list --repo <owner>/<repo> --branch <branch> --limit 1 --json conclusion,status,name,databaseId
+
+# View failure logs for the latest failed run
+gh run view --repo <owner>/<repo> --log-failed \
+  $(gh run list --repo <owner>/<repo> --branch <branch> --limit 1 --json databaseId --jq '.[0].databaseId')
+
+# Wait for a specific run (never use sleep)
+gh run watch --repo <owner>/<repo> <run-id>
+```
+```pwsh
+# PowerShell
+$runId = (gh run list --repo <owner>/<repo> --branch <branch> --limit 1 --json databaseId | ConvertFrom-Json).databaseId
+gh run watch --repo <owner>/<repo> $runId
+```
+
+**Reading status:**
+- `conclusion: success` — green
+- `conclusion: failure` — red; use `--log-failed` to triage
+- `conclusion: null` + `status: in_progress` — still running; use `gh run watch`
+- `conclusion: cancelled` — was aborted; re-run if stale
+
+---
+
+## 2. Open PRs and review status
+```bash
+# List all open PRs with review state
+gh pr list --repo <owner>/<repo> --state open --json number,title,reviewDecision,statusCheckRollup,author
+
+# PRs with failed CI
+gh pr list --repo <owner>/<repo> --state open --json number,title,statusCheckRollup \
+  --jq '[.[] | select(.statusCheckRollup[] | .conclusion == "FAILURE")]'
+
+# PRs awaiting review (no decision yet)
+gh pr list --repo <owner>/<repo> --state open --json number,title,reviewDecision \
+  --jq '[.[] | select(.reviewDecision == null or .reviewDecision == "REVIEW_REQUIRED")]'
+
+# Full PR detail
+gh pr view <number> --repo <owner>/<repo>
+gh pr checks <number> --repo <owner>/<repo>   # all CI check results for a PR
+```
+
+**Review decision values:**
+- `APPROVED` — at least one approval, no blockers
+- `CHANGES_REQUESTED` — blocked by reviewer
+- `REVIEW_REQUIRED` — no reviews yet
+- `null` — no review policy configured
+
+---
+
+## 3. CodeQL / code-scanning alerts
+```bash
+# All open code-scanning (CodeQL) alerts
+gh api /repos/<owner>/<repo>/code-scanning/alerts?state=open --paginate \
+  --jq '.[] | {number: .number, rule: .rule.id, severity: .rule.severity, file: .most_recent_instance.location.path}'
+
+# High/critical only
+gh api "/repos/<owner>/<repo>/code-scanning/alerts?state=open&severity=high" --paginate
+gh api "/repos/<owner>/<repo>/code-scanning/alerts?state=open&severity=critical" --paginate
+
+# Dismiss a false-positive alert (requires security_events permission)
+gh api --method PATCH /repos/<owner>/<repo>/code-scanning/alerts/<number> \
+  -f dismissed_reason='false positive' \
+  -f dismissed_comment='CodeQL does not track custom sanitizer <function_name>'
+
+# Alert count summary
+gh api /repos/<owner>/<repo>/code-scanning/alerts?state=open --paginate --jq 'length'
+```
+
+**Severity triage order:** `critical` → `high` → `error` → `warning` → `note`
+
+---
+
+## 4. Dependabot alerts
+```bash
+# All open Dependabot vulnerability alerts
+gh api /repos/<owner>/<repo>/dependabot/alerts?state=open --paginate \
+  --jq '.[] | {number: .number, severity: .security_advisory.severity, package: .dependency.package.name, cve: .security_advisory.cve_id}'
+
+# Critical/high only
+gh api "/repos/<owner>/<repo>/dependabot/alerts?state=open&severity=critical" --paginate
+gh api "/repos/<owner>/<repo>/dependabot/alerts?state=open&severity=high" --paginate
+
+# Check for auto-generated Dependabot PRs
+gh pr list --repo <owner>/<repo> --author 'dependabot[bot]' --state open
+
+# Dismiss an alert (requires correct permission)
+gh api --method PATCH /repos/<owner>/<repo>/dependabot/alerts/<number> \
+  -f state=dismissed \
+  -f dismissed_reason='tolerable_risk' \
+  -f dismissed_comment='Not reachable in production'
+```
+
+**Severity triage order:** `critical` → `high` → `medium` → `low`
+
+---
+
+## 5. Code quality / policy violations
+```bash
+# Repository rule violations (branch protection)
+gh api /repos/<owner>/<repo>/rules/branches/<branch> 2>/dev/null | \
+  jq '.rules[] | {type: .type, enforcement: .enforcement}'
+
+# Recent workflow runs with bypass violations
+gh run list --repo <owner>/<repo> --limit 20 --json event,conclusion,displayTitle \
+  --jq '[.[] | select(.conclusion == "failure")]'
+
+# Check branch protection status
+gh api /repos/<owner>/<repo>/branches/<branch>/protection 2>/dev/null
+
+# Secret scanning alerts (requires advanced security)
+gh api /repos/<owner>/<repo>/secret-scanning/alerts?state=open 2>/dev/null --paginate
+```
+
+---
+
+## Full health snapshot (one-shot)
+```bash
+#!/usr/bin/env bash
+REPO="<owner>/<repo>"
+BRANCH="<branch>"
+
+echo "=== CI (latest 3 runs) ==="
+gh run list --repo $REPO --branch $BRANCH --limit 3
+
+echo "=== Open PRs ==="
+gh pr list --repo $REPO --state open --json number,title,reviewDecision,author \
+  --jq '.[] | "#\\(.number) \\(.title) [\\(.reviewDecision // "NO_REVIEW")] by \\(.author.login)"'
+
+echo "=== CodeQL alerts (open) ==="
+gh api /repos/$REPO/code-scanning/alerts?state=open --paginate --jq 'length'
+
+echo "=== Dependabot alerts (open) ==="
+gh api /repos/$REPO/dependabot/alerts?state=open --paginate --jq 'length' 2>/dev/null || echo "N/A"
+```
+
+---
+
+## Key rules
+- **Always triage in order**: CI → PRs → CodeQL → Dependabot → policy.
+- Never dismiss a CodeQL alert as false positive without a specific comment explaining why.
+- Dependabot `tolerable_risk` dismissals require a comment with the CVE and reachability rationale.
+- `gh api` requires the `repo` or `security_events` scope depending on alert type.
+- Check `gh auth status` first if any API calls return 401/403.
+""",
+    ),
     SkillEntry(
         slug="github-actions-ci",
         name="GitHub Actions CI — Layer1Labs pattern (zero-trust, parallel, coverage-gated)",
@@ -40,7 +226,9 @@ Reference implementation: `chronomemory/.github/workflows/ci.yml`
 - `permissions: contents: read` on each individual job — grant minimum needed.
 - All jobs run **in parallel** — no `needs:` dependency chain unless truly required.
 - Full Python matrix: **3.10, 3.11, 3.12, 3.13** × ubuntu-latest, windows-latest.
-- Coverage gate: `--cov-fail-under=85`.
+- Coverage gate: `--cov-fail-under=85` when the project can sustain it.
+  Omit or lower the threshold for large codebases with integration-heavy code
+  (e.g. CLI drivers, HTTP servers) that are structurally hard to unit-test.
 - Named jobs (`name:` field) for readable GitHub UI.
 - `fail-fast: false` on the test matrix so all combinations are reported.
 
@@ -108,6 +296,8 @@ jobs:
           cache: pip
       - run: pip install -e ".[dev]"
       - run: pytest --cov=<package> --cov-report=term-missing --cov-fail-under=85
+      # Note: omit --cov-fail-under when coverage is below 85% structurally
+      # (large CLIs/servers with hard-to-unit-test paths).
 
   security:
     name: Security audit (pip-audit)
@@ -129,7 +319,9 @@ jobs:
 - Do NOT set `permissions: contents: read` at workflow level — use `permissions: {}` + per-job grants.
 - Do NOT use `needs: [lint, typecheck]` to gate the test job — run all in parallel.
 - Do NOT omit Python 3.11 from the matrix.
-- Do NOT skip `--cov-fail-under` — the 85% gate is non-negotiable.
+- Do NOT skip `--cov-fail-under` when unit coverage can sustain 85%.
+  For large codebases with structural coverage limits, omit it rather than
+  carrying a perpetually-failing gate.
 - Do NOT use `cancel-in-progress: true` (concurrency block) unless there is a
   specific reason — chronomemory pattern omits it.
 - Do NOT use `macos-latest` in the matrix unless macOS-specific behavior must be

{specsmith-0.11.3.dev432 → specsmith-0.11.3.dev435}/src/specsmith/skills/governance.py

@@ -390,6 +390,146 @@ gh run list --repo <owner>/<repo> --branch <branch> --limit 1 --json databaseId,
 """
         ),
     ),
+    SkillEntry(
+        slug="patent-prosecution-workflow",
+        name="Patent Prosecution Workflow — prior-art protocol, USPTO MCP, claim themes",
+        description=(
+            "IP prosecution workflow for patent-prosecution type projects: prior-art protocol "
+            "execution, USPTO MCP server selection, PPUBS\u2192PatentsView fallback, PAR ID "
+            "assignment, claim theme tracking, and ledger entry format."
+        ),
+        domain=SkillDomain.GOVERNANCE,
+        tags=[
+            "patent",
+            "patent-prosecution",
+            "prior-art",
+            "uspto",
+            "mcp",
+            "ppubs",
+            "patentsview",
+            "claim-themes",
+            "ip",
+            "par",
+        ],
+        prerequisites=[],
+        body="""\
+# Patent Prosecution Workflow Skill
+
+For use with `type: patent-prosecution` projects (e.g. cpsc-core).
+All MCP tool outputs are INFORMATIONAL. Never alter normative specifications
+based on MCP output. No legal conclusions from tool output.
+
+## Prior-art protocol trigger
+
+When a user issues a command beginning with `prior-art protocol:`, follow
+this sequence:
+
+1. Re-read the current protocol text from `docs/ip/prosecution/` and `docs/ip/strategy/`.
+2. Identify which themes/claims are covered and which MCP sources are available.
+3. Execute the relevant portions using the appropriate MCP servers (see selection below).
+4. Assign a Run ID: `PAR-YYYY-MM-DD-NNN` (e.g. `PAR-2026-05-19-001`).
+5. Append a ledger entry (see format below).
+
+Recognised command patterns (not a closed list):
+```
+prior-art protocol: start Themes A-H (PPUBS only)
+prior-art protocol: start Themes A-H (PTAB+PFW+CitA only)
+prior-art protocol: status (USPTO MCP)
+prior-art protocol: rerun since <reason> (USPTO MCP)
+```
+
+## MCP server selection matrix
+
+| Need | Server |
+|---|---|
+| Front-door full-text patent search | `patents` (PPUBS / PatentsView) |
+| PatentsView landscape query (CPC) | `patents` (`patentsview_search_by_cpc`) |
+| PTAB trial / appeal research | `uspto_ptab` |
+| File-wrapper, claim evolution, NOAs, office actions, examiner citations | `uspto_pfw` |
+| Final petition decisions | `uspto_fpd` |
+| Enriched citation analysis | `uspto_enriched_citations` |
+
+For theme-based prior-art protocols: treat `uspto_ptab`, `uspto_pfw`, `uspto_fpd`,
+`uspto_enriched_citations` as **primary** structured sources. Treat `patents`
+(PPUBS/PatentsView) as **complementary** front-door search.
+
+## PPUBS → PatentsView fallback
+
+When `patents` MCP returns HTTP 500 `INTERNAL_SERVER_ERROR` with
+`"Unable to Process"` developer message:
+
+1. This is an **upstream PPUBS service issue** — not a misconfiguration.
+2. Immediately fall back to `patentsview_search_patents` (or `patentsview_search_by_cpc`).
+3. Continue the protocol using PatentsView + USPTO v3 MCP servers.
+4. Note explicitly in the response: *PPUBS 500 — results based on PatentsView / USPTO MCP*.
+
+PPUBS 500s MUST NOT block prior-art protocol execution.
+
+## Claim theme tracking
+
+Themes are defined in `scaffold.yml` under `claim_themes`. Each theme has:
+- `id` — letter (A, B, C...)
+- `name` — human description
+- `risk` — `101-alice`, `103-low`, `103-moderate-high`, `none`, etc.
+- `primary_comparator` — US patent number or null
+- `last_par_run` — PAR ID of the most recent covering run
+
+Before running a protocol, check which themes have stale `last_par_run`
+values (run predates the most recent spec update).
+
+## PAR ID format
+
+```
+PAR-YYYY-MM-DD-NNN
+PAR-2026-05-19-001  # first run on 2026-05-19
+PAR-2026-05-19-002  # second run same day
+```
+
+Increment NNN by scanning existing PAR entries in `docs/LEDGER.md`.
+
+## Ledger entry format (append to docs/LEDGER.md)
+
+```markdown
+## PAR-YYYY-MM-DD-NNN — Prior-Art Run
+
+- **Date**: YYYY-MM-DD
+- **Trigger**: <user command or reason>
+- **Themes**: A, B, C (or ALL)
+- **MCP sources**: PPUBS, PatentsView, uspto_ptab, uspto_pfw, uspto_fpd, uspto_enriched_citations
+- **Risk levels**: Theme A: 101-alice — Theme B: 103-moderate-high — ...
+- **Conclusion summary**: <1-3 sentence summary of findings>
+- **Stale themes post-run**: <list any themes needing re-run or NONE>
+```
+
+## Prosecution phases (patent-prosecution lifecycle)
+
+| Phase | Key milestone |
+|---|---|
+| `provisional-draft` | Invention disclosure written; at least one embodiment documented |
+| `filing` | Filed PDF in `docs/ip/filings/`; SHA-256 recorded in LEDGER.md |
+| `prior-art-search` | All themes searched; each has ≥1 PAR run; risk levels assigned |
+| `claim-hardening` | PAR findings applied to draft claims; counsel reviewed |
+| `non-provisional-draft` | Draft complete; figures rendered; claim set approved by counsel |
+| `examination` | Filed non-provisional; examiner assigned; responding to OAs |
+| `allowance` | NOA received OR continuation filed |
+
+## Roles (agents in IP repos)
+
+| Role | What they may do |
+|---|---|
+| **Spec Drafter** | Draft spec text; NOT finalize |
+| **Reviewer** | Analyze, comment; NOT modify normative text |
+| **Example Generator** | Non-normative folders only |
+| **Implementation Assistant** | Cannot modify specs |
+
+## Invariants (NEVER violate)
+- No legal conclusions from MCP tool output.
+- No new semantics introduced without inventor approval.
+- Filed artifacts in `docs/ip/filings/` are immutable.
+- Normative content lives under `docs/ip/specs/` only.
+- Experiment data belongs in `cpsc-engine-rtl`, not cpsc-core.
+""",
+    ),
     SkillEntry(
         slug="issue-triage",
         name="Issue Triage — classify and prioritise GitHub issues",

{specsmith-0.11.3.dev432 → specsmith-0.11.3.dev435}/src/specsmith/tools.py

@@ -311,6 +311,14 @@ _TOOL_REGISTRY: dict[ProjectType, ToolSet] = {
         build=["vivado -mode batch"],
         format=["ruff format"],
     ),
+    # --- IP / Patent prosecution ---
+    ProjectType.PATENT_PROSECUTION: ToolSet(
+        lint=["vale", "cspell"],
+        format=["prettier"],
+        build=["pandoc"],
+        compliance=["specsmith trace verify", "claim-ref-check"],
+        test=["markdown-link-check"],
+    ),
     # --- AEE / Epistemic project types ---
     ProjectType.EPISTEMIC_PIPELINE: ToolSet(
         lint=["ruff check", "specsmith stress-test"],

{specsmith-0.11.3.dev432 → specsmith-0.11.3.dev435/src/specsmith.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: specsmith
-Version: 0.11.3.dev432
+Version: 0.11.3.dev435
 Summary: Applied Epistemic Engineering toolkit — AEE agent sessions, execution profiles, FPGA/HDL governance, tool installer, 50+ CLI commands.
 Author: BitConcepts
 License-Expression: MIT