diff --git a/.github/tools/clean_lint_sarif.py b/.github/tools/clean_lint_sarif.py
index f34272d762..e8f31d8acd 100755
--- a/.github/tools/clean_lint_sarif.py
+++ b/.github/tools/clean_lint_sarif.py
@@ -36,6 +36,7 @@
 """
 
 import argparse
+import hashlib
 import json
 import os
 import re
@@ -159,7 +160,11 @@ def main():
         if result_count == 0:
             continue
 
-        out_name = path.replace(os.sep, "__") + ".sarif"
+        # Flattening a deeply-nested Bazel output path into one filename can
+        # exceed the filesystem's filename length limit; hash it instead.
+        # The name only needs to be unique, since the merge step globs
+        # every ".sarif" file in the tool's output directory.
+        out_name = hashlib.sha1(path.encode()).hexdigest() + ".sarif"
         with open(os.path.join(args.output_dir, out_name), "w", encoding="utf-8") as f:
             json.dump(report, f)
         written += 1
diff --git a/.github/tools/manual_lint_targets.sh b/.github/tools/manual_lint_targets.sh
new file mode 100755
index 0000000000..7581f6966c
--- /dev/null
+++ b/.github/tools/manual_lint_targets.sh
@@ -0,0 +1,54 @@
+#!/usr/bin/env bash
+# *******************************************************************************
+# Copyright (c) 2026 Contributors to the Eclipse Foundation
+#
+# See the NOTICE file(s) distributed with this work for additional
+# information regarding copyright ownership.
+#
+# This program and the accompanying materials are made available under the
+# terms of the Apache License Version 2.0 which is available at
+# https://www.apache.org/licenses/LICENSE-2.0
+#
+# SPDX-License-Identifier: Apache-2.0
+# *******************************************************************************
+# Finds `manual`-tagged targets that a linter aspect would otherwise apply
+# to, and prints their labels one per line.
+#
+# `manual` only excludes a target from wildcards like `//...`; rules_lint's
+# aspects don't check for it. Building the target by name is the only way to
+# lint it, so the lint workflow appends this script's output to its build.
+#
+# docs()/docs_bundle() wrapper targets are excluded: their srcs are external
+# repo code, nothing here to lint. Platform-incompatible targets are excluded
+# too, since naming one explicitly fails the build instead of being skipped.
+#
+# Usage: manual_lint_targets.sh <bazel-build-config>
+set -euo pipefail
+
+config="${1:?usage: manual_lint_targets.sh <bazel-build-config>}"
+
+# Rule kinds each linter aspect visits: clang-tidy (cc_*), Ruff (py_*),
+# Clippy (rust_*).
+lintable_kinds='cc_binary|cc_library|cc_test|py_binary|py_library|py_test|rust_binary|rust_library|rust_shared_library|rust_test'
+
+# \b avoids matching tags that merely contain "manual", e.g. "manually".
+query="attr(tags, '\bmanual\b', kind('${lintable_kinds}', //...))"
+query+=" except attr(generator_function, '^docs', //...)"
+
+mapfile -t candidates < <(bazel query "${query}")
+
+if [ ${#candidates[@]} -eq 0 ]; then
+    exit 0
+fi
+
+# cquery, not query, since compatibility is only known after configuration.
+# Prints the label if compatible, else a blank line, which gets dropped below.
+print_label_if_compatible='(
+    "" if "IncompatiblePlatformProvider" in [str(type(p)) for p in providers(target).values()]
+    else "//{}:{}".format(target.label.package, target.label.name)
+)'
+
+bazel cquery --config="${config}" "set(${candidates[*]})" \
+    --output=starlark \
+    --starlark:expr="${print_label_if_compatible}" \
+    | sed '/^$/d'
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 76f42ecf30..ed07d7c6b4 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -14,6 +14,8 @@
 # Runs clang-tidy, Clippy, and Ruff through rules_lint in one job. Each build
 # uses fail_on_violation=false so violating targets still produce SARIF; the
 # job fails at the end, once everything has been collected and uploaded.
+# `manual` targets are built separately, by name, since `//...` skips them;
+# see .github/tools/manual_lint_targets.sh.
 name: Linter checks
 permissions:
   contents: read
@@ -46,6 +48,14 @@ jobs:
           bazel build --config=bl-x86_64-linux --config=lint --keep_going \
             --output_groups=+rules_lint_machine --@aspect_rules_lint//lint:fail_on_violation=false \
             -- //...
+      - name: Bazel build with linters (manual targets)
+        run: |
+          mapfile -t manual_targets < <(.github/tools/manual_lint_targets.sh bl-x86_64-linux)
+          if [ "${#manual_targets[@]}" -gt 0 ]; then
+            bazel build --config=bl-x86_64-linux --config=lint --keep_going \
+              --output_groups=+rules_lint_machine --@aspect_rules_lint//lint:fail_on_violation=false \
+              -- "${manual_targets[@]}" || true
+          fi
       - name: Collect human-readable lint reports
         if: always()
         run: |