deps: bump ruff from 0.15.20 to 0.16.0

README.md

@@ -194,7 +194,10 @@ from agents.mcp import MCPServerStdio
 
 async with MCPServerStdio(
     name="cortex",
-    params={"command": "uvx", "args": ["--from", "hypermnesia-mcp[sqlite]", "hypermnesia-mcp"]},
+    params={
+        "command": "uvx",
+        "args": ["--from", "hypermnesia-mcp[sqlite]", "hypermnesia-mcp"],
+    },
 ) as server:
     agent = Agent(name="Assistant", mcp_servers=[server])
 ```

docs/papers/research-post-context-assembly.md

@@ -1227,10 +1227,13 @@ BEAM paper.  See commit `5348f74`.
 the harness verifies FlashRank by reranking a synthetic pair:
 
 ```python
-result = flashrank.rerank([
-    {"content": "The cat sat on the mat", "score": 0.0},
-    {"content": "Dogs are loyal pets", "score": 0.0},
-], query="What did the cat do?")
+result = flashrank.rerank(
+    [
+        {"content": "The cat sat on the mat", "score": 0.0},
+        {"content": "Dogs are loyal pets", "score": 0.0},
+    ],
+    query="What did the cat do?",
+)
 assert result[0]["score"] > 0, "FlashRank model loading failed"
 ```
 

docs/program/phase-0.4.5-backfill-design.md

@@ -256,9 +256,12 @@ Intended shape for `mcp_server/handlers/consolidation/reconcile.py`:
 ```python
 def run_reconcile_cycle(store) -> dict:
     from mcp_server.core.entity_reconciliation import (
-        build_reconciliation_sql, build_count_eligible_sql,
-        reconcile_leak_ratio, exceeds_leak_threshold,
+        build_reconciliation_sql,
+        build_count_eligible_sql,
+        reconcile_leak_ratio,
+        exceeds_leak_threshold,
     )
+
     count_sql, params = build_count_eligible_sql()
     eligible = store.execute_scalar(count_sql, params)
     insert_sql, params = build_reconciliation_sql()
@@ -268,7 +271,8 @@ def run_reconcile_cycle(store) -> dict:
         logger.warning(
             "reconcile leak ratio %.3f exceeds threshold %.3f; "
             "investigate write path (persist_entities)",
-            ratio, LEAK_WARNING_THRESHOLD,
+            ratio,
+            LEAK_WARNING_THRESHOLD,
         )
     return {
         "reconciled_pairs": reconciled,

docs/program/phase-3-a3-migration-design.md

@@ -295,8 +295,7 @@ def bump_heat_raw(self, memory_id: int, new_heat_base: float) -> None:
     compute decay from the bump time, not the row's previous anchor.
     """
     self._execute(
-        "UPDATE memories SET heat_base = %s, heat_base_set_at = NOW() "
-        "WHERE id = %s",
+        "UPDATE memories SET heat_base = %s, heat_base_set_at = NOW() WHERE id = %s",
         (max(0.0, min(1.0, new_heat_base)), memory_id),
     )
     self._conn.commit()
@@ -314,7 +313,8 @@ calls `bump_heat_raw` per-row (rare — only memify / replay / rating).
 
 **Current**:
 ```python
-"UPDATE memories SET heat = 1.0, is_protected = TRUE, importance = 1.0, "
+"UPDATE memories SET heat = 1.0, is_protected = TRUE, importance = 1.0,"
+
 "tags = %s::jsonb, content = %s, is_global = %s WHERE id = %s"
 ```
 
@@ -324,7 +324,8 @@ rows ignore decay in `effective_heat()` and always return
 `LEAST(1.0, heat_base * factor) = 1.0` at `factor = 1.0`.
 
 ```python
-"UPDATE memories SET heat_base = 1.0, heat_base_set_at = NOW(), "
+"UPDATE memories SET heat_base = 1.0, heat_base_set_at = NOW(),"
+
 "is_protected = TRUE, no_decay = TRUE, importance = 1.0, "
 "tags = %s::jsonb, content = %s, is_global = %s WHERE id = %s"
 ```
@@ -392,7 +393,8 @@ SQLite path keeps the column but recomputes `effective_heat` in Python
 (shared `mcp_server/core/effective_heat.py`, a pure function).
 
 ```python
-"UPDATE memories SET heat_base = ?, heat_base_set_at = CURRENT_TIMESTAMP "
+"UPDATE memories SET heat_base = ?, heat_base_set_at = CURRENT_TIMESTAMP"
+
 "WHERE id = ?"
 ```
 

docs/program/phase-5-pool-admission-design.md

@@ -81,7 +81,7 @@ Today:
 ```python
 async def handler(args: dict) -> dict:
     store = _get_store()
-    return store.do_sync_work(args)   # blocks event loop
+    return store.do_sync_work(args)  # blocks event loop
 ```
 
 Post-Phase 5:
@@ -102,14 +102,15 @@ Each tool declares a concurrency budget. The MCP server registers a
 
 ```python
 _ADMISSION: dict[str, asyncio.Semaphore] = {
-    "recall":              asyncio.Semaphore(8),
-    "remember":            asyncio.Semaphore(4),
-    "consolidate":         asyncio.Semaphore(1),   # one at a time
-    "seed_project":        asyncio.Semaphore(1),
-    "wiki_pipeline":       asyncio.Semaphore(1),
+    "recall": asyncio.Semaphore(8),
+    "remember": asyncio.Semaphore(4),
+    "consolidate": asyncio.Semaphore(1),  # one at a time
+    "seed_project": asyncio.Semaphore(1),
+    "wiki_pipeline": asyncio.Semaphore(1),
     # default: Semaphore(4) for interactive, Semaphore(1) for batch
 }
 
+
 async def admit(tool_name: str, coro):
     sem = _ADMISSION.get(tool_name, _default_for_class(tool_name))
     async with sem:

docs/provenance/pyright-remediation-plan.md

@@ -326,8 +326,10 @@ authors.
    Fails if any rule in --blocking has a current count > baseline count.
    Reports all rules showing count deltas.
    """
+
    import json, sys, argparse
 
+
    def main():
        p = argparse.ArgumentParser()
        p.add_argument("current")
@@ -368,6 +370,7 @@ authors.
            sys.exit(1)
        print("\nPASS: no regressions in blocking rules")
 
+
    if __name__ == "__main__":
        main()
    ```

docs/testing-guide.md

@@ -234,10 +234,13 @@ Async functions are tested via `asyncio.get_event_loop().run_until_complete()`:
 def _run(coro):
     return asyncio.get_event_loop().run_until_complete(coro)
 
+
 class TestMcpRouter:
     def test_returns_server_info(self):
         router = create_router(mock_registry)
-        response = _run(router({"jsonrpc": "2.0", "id": 1, "method": "initialize", "params": {}}))
+        response = _run(
+            router({"jsonrpc": "2.0", "id": 1, "method": "initialize", "params": {}})
+        )
         parsed = json.loads(response)
         assert parsed["result"]["serverInfo"]["name"] == "methodology-agent"
 ```

pyproject.toml

@@ -585,7 +585,7 @@ dev = [
 # to dependencies: a lint job that drags in pyright pays for it in cold-start
 # time and in supply-chain surface).
 lint = [
-    "ruff==0.15.20",
+    "ruff==0.16.0",
 ]
 typecheck = [
     "pyright==1.1.410",

requirements/lint.txt

@@ -10,22 +10,22 @@
 ##########################################################################
 # This file was autogenerated by uv via the following command:
 #    uv export --locked --no-emit-project --no-default-groups --format requirements.txt --only-group lint
-ruff==0.15.20 \
-    --hash=sha256:00e188c53e499c3c1637f73c91dcf2fb56d576cab76ce1be50a27c4e80e37078 \
-    --hash=sha256:01cc00dd58f0df339d0e902219dd53990ea99996a0344e5d9cc8d45d5307e460 \
-    --hash=sha256:1416eb04349192646b54de98f146c4f59afe37d0decfc02c3cbbf396f3a28566 \
-    --hash=sha256:2d2374caa2f2c2f9e2b7da0a50802cfb8b79f55a9b5e49379f564544fbf56487 \
-    --hash=sha256:2f5b2a6d614e8700388806a14996c40fab2c47b819ef57d790a34878858ed9ca \
-    --hash=sha256:309809086c2acb67624950a3c8133e80f32d0d3e27106c0cd60ff26657c9f24b \
-    --hash=sha256:3413bb3c3d2ca6a8208f1f4809cd2dca3c6de6d0b491c0e70847672bde6e6efd \
-    --hash=sha256:5b9c0c367ad8e5d0d5b5b8537864c469a0a0e55417aadfbeca41fa61333be9f4 \
-    --hash=sha256:9ebd1fd9b9c95fc0bd7b2761aebec1f030013d2e193a2901b224af68fe47251b \
-    --hash=sha256:a1ed17b65293e0c2f22fc387bc13198a5de94bf4429589b0ff6946b0feaf21a3 \
-    --hash=sha256:a525c81c70fb0380344dd1d8745d8cc1c890b7fc94a58d5a07bd8eb9557b8415 \
-    --hash=sha256:b6df3b1e4610432f0386dba04d853b5f08cbbc903410c6fcc02f620f05aff53c \
-    --hash=sha256:bd7ec42b3bb3da066488db093308a69c4ac5ee6d2af333a86ba6e2eb2e7dd44b \
-    --hash=sha256:c5b16cdd67ca108185cd36dce98c576350c03b1660a751de725fb049193a0632 \
-    --hash=sha256:e1a36ad0eb77fba9aabfb69ede54de6f376d04ac18ebea022847046d340a8267 \
-    --hash=sha256:e89f198a1ea6ef0d727c1cf16088bc91a6cb0ab947dedc966715691647186eae \
-    --hash=sha256:ed65ef510e43a137207e0f01cfcf998aeddb1aeeda5c9d35023e910284d7cf21 \
-    --hash=sha256:f701305e66b38ea6c91882490eb73459796808e4c6362a1b765255e0cdcd4053
+ruff==0.16.0 \
+    --hash=sha256:0ff4a79ce3ec0172f3241943835de1c4cb4e2dcd07f0f8c2d02603dbbbee4b17 \
+    --hash=sha256:14296fedcd2705c77ab8235439278bbb38f285cf7da5528b00b3e330c3d4872d \
+    --hash=sha256:28ea2b7df8ebf7f9da6b7d47b230ab48f387c0a29be3b474c4d0740e197bb9af \
+    --hash=sha256:33a3dfac8c35f81498dea9181bccc2f4c4bc8f1521a1dd9406e77643e0f0fb09 \
+    --hash=sha256:3c954b1d580bfa035b41654f7858cc7e71d5fc3ac5b723dd62bd9133830ed522 \
+    --hash=sha256:429c117f022bf481fabd9d551e7a3952b24c65e6ef44337ea09d90bebef14472 \
+    --hash=sha256:48044c678e9cb8698246c99b14aaccfa6601dea7379eb48a6f8f73f7a6d86cd0 \
+    --hash=sha256:4f11a8d11010301d0a398a2fdef67691feca7294da6aef55e2150e8fa2cd520b \
+    --hash=sha256:6e364e5ed22ed8dc05082fd78e35308618260907ac2d3c1d637b2e682415b6c9 \
+    --hash=sha256:7aa0959bad8eb8bef50340154fc9b58678dae31fa4293afa38b44b6e552c0213 \
+    --hash=sha256:7fab76fa065c873f41ff744347c6e77bcc3dfec4bcc754dc26b63d23c0f7f5fb \
+    --hash=sha256:a5237a0bda500d30d81b8e07a6973a5cbc772864cbf746ae2f4e8a2e01c9f4ed \
+    --hash=sha256:a9b50c55e263103586b3dcf5f73d479eb8cb5fdb6098fec59a62891dab653717 \
+    --hash=sha256:d327b8fc113a1d4421a04f3839d3752057c8dd1ee320223a6f3f52d04ada462a \
+    --hash=sha256:e01c21d10eb1b29f47b7454e1f4056db9a3f0260c646aa88457c610291db9f81 \
+    --hash=sha256:e460aafd5495ec89efaa6ced2e4a9a581116451e1c88b9d37ef497e0f8e93982 \
+    --hash=sha256:e5115729eb08c585e5121978ba5d5b60caeae394ce21b9fb5e6cd33a1c6c9b1e \
+    --hash=sha256:e95c448fca1fb2a18372a9440926c5a6ee789639bb975c72e7ae6d0b04218ab4