Bump persistency to latest main (upstream test-venv fix) and refresh overrides (#388)

* Enable persistency integration tests and fix test-venv pip hub collision

The score_persistency KVS integration tests (//score/kvs/tests/test_cases:cit,
i.e. cit_cpp + cit_rust) could not build in reference_integration: building
their test venv failed with

    × Collision resolution not yet implemented!
      Saw nodejs_wheel/bin/corepack twice   (then iniconfig, pytest, ...)

Root cause: the venv is assembled by score_tooling's score_virtualenv, which
does py_venv(deps = <@pip_tooling all_requirements> + reqs + ...). persistency
passes reqs = all_requirements of its own test hub (@pip_score_persistency_venv_test,
renamed by patch 003). That hub re-vendors score_tooling's
python_basics/requirements.txt (the test lock lists it as a compile src), so
basedpyright, iniconfig, nodejs-wheel-binaries, packaging, pluggy, pygments and
pytest exist in BOTH hubs. aspect_rules_py 1.5.2's venv tool cannot merge two
different repos that ship the same file (collision resolution is unimplemented
regardless of package_collisions=warning/ignore), so venv creation aborts.

This surfaced only after persistency was bumped to 323950c (#383) and the module
integration-test step was added (#385); it is the first time these tests ran in
reference_integration.

Fix (patches/persistency/006-dedupe-test-venv-pip-hub.patch): drop the seven
packages that score_tooling's @pip_tooling hub already provides from persistency's
test lock, so each package is contributed by exactly one hub. pytest and friends
come from @pip_tooling (added by score_virtualenv); persistency's hub keeps only
its own unique deps (psutil, pytest-env, pytest-html, pytest-metadata,
pytest-repeat, testing-utils, jinja2, markupsafe).

Verified locally (no docker): both
@score_persistency//score/kvs/tests/test_cases:python_tc_venv and
@score_persistency//score/kvs/tests/test_cases:cit build successfully with the
patch applied.

Re-enable the persistency integration_test_targets/integration_test_config in
known_good.json (removed in #386) so CI exercises the KVS integration tests.

* Bump persistency to latest main and refresh integration-test overrides

persistency fixed the test-venv pip hub collision upstream (#463 migrated
to score_pytest from score_tools, #466 renamed the hub to
pip_score_persistency_venv_test and dropped the unused python_tc_venv IDE
venv). Bump the pinned commit to current main (961c0a0) so the
reference_integration graph picks up those fixes directly.

Consequences of the bump:
- Drop 006-dedupe-test-venv-pip-hub.patch: the colliding python_tc_venv it
  worked around no longer exists upstream.
- Regenerate 003/004/005 against the new MODULE.bazel (the old context no
  longer matched, so Bazel failed to apply them during fetch).
- Add 006-tools / 007-sbom: the new main declares score_tools and score_sbom
  as dev_dependency, but reference_integration (root) needs them non-dev
  because the test BUILD loads @score_tools//score_pytest and the module
  root BUILD loads @score_sbom//:defs.bzl.

Regenerated bazel_common/score_modules_target_sw.MODULE.bazel and refreshed
MODULE.bazel.lock accordingly.

* Pin score_tools to the $(locations) fix for persistency cit tests

Persistency's integration test //score/kvs/tests/test_cases:cit failed in
analysis:

  cit_cpp: label '...:cit_files' in $(location) expression expands to more
  than one file, please use $(locations ...) instead.

score_pytest (from score_tools) only emits the correct $(locations ...)
for multi-file srcs starting at a commit past the registry version 0.0.3.
Persistency's own MODULE.bazel git_overrides score_tools to 4b48cec for
exactly this fix, but Bzlmod ignores non-root overrides, so RI (root) was
resolving score_tools 0.0.3 from the registry (still buggy).

Add score_tools to known_good.json pinned to the same commit so the root
module applies the override, regenerate the tooling MODULE fragment and
refresh the lockfile.

* Consolidate persistency dev_dependency flips into one patch

The five patches 003-007 all edited the same file (MODULE.bazel) and four
of them touched the same hunk region, so none of 005/006/007 applied
standalone - they only worked as a sequential chain in exactly the
known_good.json order, each carrying the previous ones' edits as context.
Reordering or dropping any entry silently broke the rest.

Replace them with a single patch containing two clean hunks. Same net
effect: flip googletest, score_sbom, score_rules_imagefs, score_tools and
the pip extension to non-dev, because their apparent names appear in
BUILD/.bzl files that reference_integration evaluates (//:BUILD for the
docs bundle, test_cases/BUILD for the pip hub). Extensions RI never
evaluates, such as sbom_metadata and imagefs, stay dev on purpose.

Verified: the patch applies standalone, and both
@score_persistency//score/kvs/tests/test_cases:cit and
@score_persistency//:docs_bundle resolve with --lockfile_mode=error.

Author: antonkri

MODULE.bazel.lock

@@ -43,12 +43,10 @@ git_override(
 bazel_dep(name = "score_persistency")
 git_override(
     module_name = "score_persistency",
-    commit = "323950c42431956ce76bf48c407a1709f114876d",
+    commit = "961c0a0989755a1e0fe8de55e83c0a44e2e20b56",
     patch_strip = 1,
     patches = [
-        "//patches/persistency:003-pip-not-dev-dependency.patch",
-        "//patches/persistency:004-imagefs-not-dev-dependency.patch",
-        "//patches/persistency:005-googletest-not-dev-dependency.patch",
+        "//patches/persistency:003-undev-deps-for-root-module.patch",
     ],
     remote = "https://github.com/eclipse-score/persistency.git",
 )

bazel_common/score_modules_target_sw.MODULE.bazel

@@ -28,6 +28,13 @@ git_override(
     remote = "https://github.com/eclipse-score/itf.git",
 )
 
+bazel_dep(name = "score_tools")
+git_override(
+    module_name = "score_tools",
+    commit = "4b48cec400c67be75cfc3fa4658ac6a0489bf7a8",
+    remote = "https://github.com/eclipse-score/tools.git",
+)
+
 bazel_dep(name = "score_tooling")
 git_override(
     module_name = "score_tooling",

bazel_common/score_modules_tooling.MODULE.bazel

@@ -61,9 +61,7 @@
             "score_persistency": {
                 "repo": "https://github.com/eclipse-score/persistency.git",
                 "bazel_patches": [
-                    "//patches/persistency:003-pip-not-dev-dependency.patch",
-                    "//patches/persistency:004-imagefs-not-dev-dependency.patch",
-                    "//patches/persistency:005-googletest-not-dev-dependency.patch"
+                    "//patches/persistency:003-undev-deps-for-root-module.patch"
                 ],
                 "metadata": {
                     "code_root_path": "//score/kvs/...",
@@ -77,9 +75,15 @@
                         "//score/kvs/tests/integration_test_scenarios/...",
                         "//score/kvs/tests/test_cases/..."
                     ],
-                    "rust_coverage_config": "ferrocene-coverage-per"
+                    "rust_coverage_config": "ferrocene-coverage-per",
+                    "integration_test_targets": [
+                        "//score/kvs/tests/test_cases:cit"
+                    ],
+                    "integration_test_config": [
+                        "flaky_test_attempts=3"
+                    ]
                 },
-                "hash": "323950c42431956ce76bf48c407a1709f114876d"
+                "hash": "961c0a0989755a1e0fe8de55e83c0a44e2e20b56"
             },
             "score_kyron": {
                 "repo": "https://github.com/eclipse-score/kyron.git",
@@ -189,6 +193,11 @@
                 "repo": "https://github.com/eclipse-score/itf.git",
                 "hash": "802e0186d373e0d9d67c1c9ccb1ea08952c7ad06"
             },
+            "score_tools": {
+                "repo": "https://github.com/eclipse-score/tools.git",
+                "docs": false,
+                "hash": "4b48cec400c67be75cfc3fa4658ac6a0489bf7a8"
+            },
             "score_tooling": {
                 "repo": "https://github.com/eclipse-score/tooling.git",
                 "docs": false,

known_good.json

@@ -0,0 +1,31 @@
+diff --git a/MODULE.bazel b/MODULE.bazel
+index 2649521..6c17327 100644
+--- a/MODULE.bazel
++++ b/MODULE.bazel
+@@ -38,13 +38,13 @@ bazel_dep(name = "score_coverage", version = "0.3.1", dev_dependency = True)
+ bazel_dep(name = "aspect_rules_lint", version = "2.7.2", dev_dependency = True)
+ bazel_dep(name = "buildifier_prebuilt", version = "8.5.1.3", dev_dependency = True)
+ bazel_dep(name = "google_benchmark", version = "1.9.5", dev_dependency = True)
+-bazel_dep(name = "googletest", version = "1.17.0.bcr.2", dev_dependency = True)
++bazel_dep(name = "googletest", version = "1.17.0.bcr.2")
+ bazel_dep(name = "score_bazel_cpp_toolchains", version = "1.0.3", dev_dependency = True)
+-bazel_dep(name = "score_sbom", version = "0.1.1", dev_dependency = True)
+-bazel_dep(name = "score_rules_imagefs", version = "0.1.0", dev_dependency = True)
++bazel_dep(name = "score_sbom", version = "0.1.1")
++bazel_dep(name = "score_rules_imagefs", version = "0.1.0")
+ bazel_dep(name = "score_rust_policies", version = "0.0.5", dev_dependency = True)
+ bazel_dep(name = "score_toolchains_rust", version = "0.10.0", dev_dependency = True)
+-bazel_dep(name = "score_tools", version = "0.0.3", dev_dependency = True)
++bazel_dep(name = "score_tools", version = "0.0.3")
+ 
+ # Pinned past v0.0.3 for the `$(locations)` fix in score_pytest.
+ git_override(
+@@ -62,7 +62,7 @@ python.toolchain(
+     python_version = PYTHON_VERSION,
+ )
+ 
+-pip = use_extension("@rules_python//python/extensions:pip.bzl", "pip", dev_dependency = True)
++pip = use_extension("@rules_python//python/extensions:pip.bzl", "pip")
+ pip.parse(
+     hub_name = "pip_score_persistency_venv_test",
+     python_version = PYTHON_VERSION,