chore: remove unused prior-art-template from investigation-reporting

AGENTS.md

@@ -33,12 +33,12 @@ An autonomous daemon that runs inside the devcontainer and checks for failing Gi
 - **Workflow**: Finds failing PRs → Runs `claude` with `--worktree` → Analyzes the failure (typically using `npm run lint`) → Commits the fix and replies to the PR.
 - **Requirements**: Requires GitHub CLI (`gh`) authenticated inside the devcontainer.
 
-### Skill-Bench (`agents/skill-bench/runner.sh`)
+### Skill-Bench (`skill-bench`)
 
-An autonomous test runner that executes E2E tests for the `patent-kit` skills using **TOML-based test cases**.
+A TOML-based E2E test runner for `patent-kit` skills, installed via `mise`.
 
-- **Architecture**: All execution happens inside the devcontainer. Test cases are defined in TOML format under `cases/<skill>/<test>.toml`.
-- **Workflow**: Reads test cases from `cases/*/*.toml` → Sets up isolated workspaces → Runs `claude -p` with test prompts → Evaluates results using check scripts → Generates summary in `logs/`.
-- **Usage**: `bash agents/skill-bench/runner.sh [pattern]` (default: `cases/*/*.toml`).
-- **Test Case Format**: TOML files with `test_prompt`, `timeout`, `[[setup]]`, and `[[checks]]` sections.
-- **Requirements**: Requires `yq` and `jq` commands inside the devcontainer.
+- **Architecture**: All execution happens inside the devcontainer. Test cases are defined in TOML format under `tests/<skill>/<test>.toml`.
+- **Workflow**: Reads test cases → Sets up isolated workspaces → Runs `claude -p` with test prompts → Evaluates results using built-in check types → Generates summary in `logs/`.
+- **Usage**: `mise run test` (runs all tests under `tests/`).
+- **Test Case Format**: TOML files with `test_prompt`, `timeout`, `[[setup]]`, and `[[checks]]` sections. See `skill-bench help` for available check types.
+- **Check Types**: `skill-loaded`, `skill-invoked`, `mcp-loaded`, `mcp-tool-invoked`, `mcp-success`, `tool-use`, `tool-param`, `workspace-file`, `workspace-dir`, `file-contains`, `log-contains`, `message-contains`, `db-query`.

plugin/skills/investigation-fetching/SKILL.md

@@ -37,10 +37,17 @@ internal reference files for this skill's internal use only.
 - "Get next relevant patent for evaluation"
 - "Get list of all relevant patents"
 - "Get list of relevant patents without evaluation"
+- "Count relevant patents"
+- "Count relevant patents without evaluation"
 - "Get list of unscreened patent IDs"
 - "Get next patent for claim analysis"
 - "Get elements for patent <patent-id>"
 - "Get list of patents with elements but no similarities"
+- "Count patents without similarities"
+- "Count screening progress"
+- "Count claim analysis progress"
+- "Count patents without prior arts"
+- "Count prior art progress"
 - "Search features"
 - "Search feature: <feature_name>"
 - "Execute SQL: SELECT COUNT(\*) FROM screened_patents WHERE judgment = 'relevant'"
@@ -69,10 +76,17 @@ When processing external requests, map them to internal instruction files:
 | "Get next relevant patent for evaluation"  | references/instructions/get-next-patent.md                  |
 | "Get list of relevant patents without..."  | references/instructions/get-relevant-patents.md             |
 | "Get all relevant patents"                 | references/instructions/get-relevant-patents.md             |
+| "Count relevant patents"                   | references/instructions/get-relevant-patents.md             |
+| "Count relevant patents without..."        | references/instructions/get-relevant-patents.md             |
 | "Get list of unscreened patent IDs"        | references/instructions/get-unscreened-patents.md           |
 | "Get next patent for claim analysis"       | references/instructions/get-next-claim-analysis-patent.md   |
 | "Get elements for patent..."               | references/instructions/get-elements.md                     |
 | "Get list of patents with elements but..." | references/instructions/get-patents-without-similarities.md |
+| "Count patents without similarities"       | references/instructions/get-patents-without-similarities.md |
+| "Count screening progress"                 | references/instructions/get-screening-statistics.md         |
+| "Count claim analysis progress"            | references/instructions/get-claim-analysis-statistics.md    |
+| "Count patents without prior arts"         | references/instructions/get-patents-without-prior-arts.md   |
+| "Count prior art progress"                 | references/instructions/get-prior-art-statistics.md         |
 | "Search features"                          | references/instructions/get-features.md                     |
 | "Search feature: <feature_name>"           | references/instructions/search-feature.md                   |
 
@@ -229,6 +243,9 @@ agents should NOT read these:
   - `get-elements.md`: Get elements for a specific patent
   - `get-patents-without-similarities.md`: Get list of patents with elements but no similarities
   - `get-features.md`: Get all product features
+  - `get-screening-statistics.md`: Get screening progress counts
+  - `get-claim-analysis-statistics.md`: Get claim analysis progress counts
+  - `get-prior-art-statistics.md`: Get prior art research progress counts
   - `search-feature.md`: Search for a specific feature by name
 - \*\*references/schema.md`: Database schema documentation
 

plugin/skills/investigation-fetching/references/instructions/get-claim-analysis-statistics.md

@@ -0,0 +1,39 @@
+# Get Claim Analysis Statistics
+
+## Purpose
+
+Retrieve aggregate claim analysis progress counts.
+
+## Request Pattern
+
+"Count claim analysis progress"
+
+## SQL Query
+
+```bash
+sqlite3 -json patents.db "
+SELECT
+  COUNT(DISTINCT patent_id) AS all_count,
+  SUM(CASE WHEN max_sim = 1 THEN 1 ELSE 0 END) AS limited_count,
+  SUM(CASE WHEN max_sim > 1 THEN 1 ELSE 0 END) AS not_limited_count
+FROM (
+  SELECT
+    patent_id,
+    MAX(CASE similarity_level
+      WHEN 'Significant' THEN 3
+      WHEN 'Moderate' THEN 2
+      WHEN 'Limited' THEN 1
+    END) AS max_sim
+  FROM similarities
+  GROUP BY patent_id
+);
+"
+```
+
+## Expected Output
+
+JSON array with one row:
+
+- `all_count`: Total patents with similarity results
+- `limited_count`: Patents where all similarities are Limited
+- `not_limited_count`: Patents with at least one Significant or Moderate similarity

plugin/skills/investigation-fetching/references/instructions/get-patents-without-prior-arts.md

@@ -1,8 +1,11 @@
 # Get Patents Without Prior Arts
 
-Retrieves list of patents with Moderate/Significant similarities but no prior art elements recorded yet.
+Retrieves list of patents with Moderate/Significant similarities but no prior art
+elements recorded yet.
 
-## SQL Query
+## Variations
+
+### List Patents Without Prior Arts
 
 ```bash
 sqlite3 -json patents.db "
@@ -20,14 +23,38 @@ AND e.patent_id NOT IN (
 "
 ```
 
+### Count Patents Without Prior Arts
+
+```bash
+sqlite3 -json patents.db "
+SELECT COUNT(DISTINCT e.patent_id) AS count
+FROM elements e
+WHERE e.patent_id IN (
+  SELECT s.patent_id
+  FROM similarities s
+  GROUP BY s.patent_id
+  HAVING SUM(CASE WHEN s.similarity_level = 'Limited' THEN 1 ELSE 0 END) = 0
+)
+AND e.patent_id NOT IN (
+  SELECT patent_id FROM prior_art_elements
+);
+"
+```
+
 ## Output Format
 
-JSON array of patent_ids:
+JSON array of patent_ids (for list queries):
 
 ```json
 [{ "patent_id": "US20240292070A1" }, { "patent_id": "US20240346271A1" }]
 ```
 
+JSON array with count (for count queries):
+
+```json
+[{ "count": 2 }]
+```
+
 Empty array if no patents pending:
 
 ```json

plugin/skills/investigation-fetching/references/instructions/get-patents-without-similarities.md

@@ -2,7 +2,9 @@
 
 Retrieves list of patents that have elements but no similarities recorded yet.
 
-## SQL Query
+## Variations
+
+### List Patents Without Similarities
 
 ```bash
 sqlite3 -json patents.db "
@@ -15,14 +17,33 @@ WHERE s.patent_id IS NULL;
 "
 ```
 
+### Count Patents Without Similarities
+
+```bash
+sqlite3 -json patents.db "
+SELECT COUNT(DISTINCT e.patent_id) AS count
+FROM elements e
+LEFT JOIN similarities s ON e.patent_id = s.patent_id
+  AND e.claim_number = s.claim_number
+  AND e.element_label = s.element_label
+WHERE s.patent_id IS NULL;
+"
+```
+
 ## Output Format
 
-JSON array of patent_ids:
+JSON array of patent_ids (for list queries):
 
 ```json
 [{ "patent_id": "US20240292070A1" }, { "patent_id": "US20240346271A1" }]
 ```
 
+JSON array with count (for count queries):
+
+```json
+[{ "count": 3 }]
+```
+
 Empty array if no patents pending:
 
 ```json

plugin/skills/investigation-fetching/references/instructions/get-prior-art-statistics.md

@@ -0,0 +1,82 @@
+# Get Prior Art Statistics
+
+## Purpose
+
+Retrieve aggregate prior art research progress counts, scoped to Not Limited
+patents (Significant/Moderate similarity only).
+
+## Request Pattern
+
+"Count prior art progress"
+
+## SQL Query
+
+```bash
+sqlite3 -json patents.db "
+SELECT
+  not_limited.all_count,
+  COALESCE(resolved.resolved_count, 0) AS resolved_count,
+  COALESCE(open_pat.open_count, 0) AS open_count,
+  not_limited.all_count - COALESCE(resolved.resolved_count, 0) - COALESCE(open_pat.open_count, 0) AS pending_count
+FROM (
+  SELECT COUNT(*) AS all_count
+  FROM (
+    SELECT patent_id
+    FROM similarities
+    GROUP BY patent_id
+    HAVING MAX(CASE similarity_level
+      WHEN 'Significant' THEN 3
+      WHEN 'Moderate' THEN 2
+      WHEN 'Limited' THEN 1
+    END) > 1
+  )
+) AS not_limited
+LEFT JOIN (
+  SELECT COUNT(DISTINCT patent_id) AS resolved_count
+  FROM prior_art_elements
+  WHERE relevance_level = 'Significant'
+    AND patent_id IN (
+      SELECT patent_id
+      FROM similarities
+      GROUP BY patent_id
+      HAVING MAX(CASE similarity_level
+        WHEN 'Significant' THEN 3
+        WHEN 'Moderate' THEN 2
+        WHEN 'Limited' THEN 1
+      END) > 1
+    )
+) AS resolved ON 1 = 1
+LEFT JOIN (
+  SELECT COUNT(DISTINCT patent_id) AS open_count
+  FROM prior_art_elements
+  WHERE patent_id IN (
+      SELECT patent_id
+      FROM similarities
+      GROUP BY patent_id
+      HAVING MAX(CASE similarity_level
+        WHEN 'Significant' THEN 3
+        WHEN 'Moderate' THEN 2
+        WHEN 'Limited' THEN 1
+      END) > 1
+    )
+    AND patent_id NOT IN (
+      SELECT DISTINCT patent_id
+      FROM prior_art_elements
+      WHERE relevance_level = 'Significant'
+    )
+) AS open_pat ON 1 = 1;
+"
+```
+
+## Expected Output
+
+JSON array with one row:
+
+- `all_count`: Total Not Limited patents (Significant/Moderate similarity)
+- `resolved_count`: Patents with prior art elements having Significant relevance
+- `open_count`: Patents with prior art elements but none with Significant relevance
+- `pending_count`: Not Limited patents with no prior art elements at all
+
+## Verification
+
+`all_count` = `resolved_count` + `open_count` + `pending_count`

plugin/skills/investigation-fetching/references/instructions/get-relevant-patents.md

@@ -23,10 +23,35 @@ WHERE judgment = 'relevant'
 "
 ```
 
+### Count Relevant Patents
+
+```bash
+sqlite3 -json patents.db "
+SELECT COUNT(*) AS count FROM screened_patents
+WHERE judgment = 'relevant';
+"
+```
+
+### Count Relevant Patents Without Evaluation
+
+```bash
+sqlite3 -json patents.db "
+SELECT COUNT(*) AS count FROM screened_patents
+WHERE judgment = 'relevant'
+  AND patent_id NOT IN (SELECT patent_id FROM claims);
+"
+```
+
 ## Output Format
 
-JSON array of patent_ids:
+JSON array of patent_ids (for list queries):
 
 ```json
 [{ "patent_id": "US20240292070A1" }, { "patent_id": "US20240346271A1" }]
 ```
+
+JSON array with count (for count queries):
+
+```json
+[{ "count": 5 }]
+```

plugin/skills/investigation-fetching/references/instructions/get-screening-statistics.md

@@ -0,0 +1,25 @@
+# Get Screening Statistics
+
+## Purpose
+
+Retrieve aggregate screening progress counts from the database.
+
+## Request Pattern
+
+"Count screening progress"
+
+## SQL Query
+
+```bash
+sqlite3 -json patents.db "SELECT * FROM v_screening_progress"
+```
+
+## Expected Output
+
+JSON array with one row:
+
+- `total_targets`: Total patents in targeting
+- `total_screened`: Total patents screened
+- `relevant`: Relevant patent count
+- `irrelevant`: Irrelevant patent count
+- `expired`: Expired patent count

plugin/skills/investigation-preparing/SKILL.md

@@ -4,11 +4,10 @@ description: |
   Initializes the patent investigation database and imports CSV files.
 
   Use this skill to set up the SQLite database (patents.db) before running
-  screening. Supports database initialization, CSV import, and progress queries.
+  screening. Supports database initialization and CSV import.
 
   Example usage:
   - "Initialize the patent database and import CSV files from csv/"
-  - "Get screening progress statistics"
 context: fork
 ---