feat: align Base with base-cli 0.4.0

.github/workflows/base-check.yml

@@ -104,6 +104,14 @@ jobs:
           ref: 2c5ef2c3a9edfbe2cf68d0645be65b920255abff
           path: .base/base-bash-libs
 
+      - name: Checkout base-cli source
+        if: ${{ inputs.setup-mode == 'source-checkout' }}
+        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5
+        with:
+          repository: basefoundry/base-cli
+          ref: 9f3ed25fc0991e3aa9de8411878805c122f90a11
+          path: .base/base-cli
+
       - name: Set up Python
         if: ${{ inputs.setup-mode == 'source-checkout' }}
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065
@@ -134,6 +142,7 @@ jobs:
         run: |
           python -m venv "$HOME/.base.d/base/.venv"
           "$HOME/.base.d/base/.venv/bin/python" -m pip install --upgrade pip
+          "$HOME/.base.d/base/.venv/bin/python" -m pip install --no-deps "$GITHUB_WORKSPACE/.base/base-cli"
           "$HOME/.base.d/base/.venv/bin/python" -m pip install -r requirements-dev.txt
 
       - name: Run basectl check --ci

.github/workflows/copilot-setup-steps.yml

@@ -25,6 +25,13 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5
 
+      - name: Checkout base-cli source
+        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5
+        with:
+          repository: basefoundry/base-cli
+          ref: 9f3ed25fc0991e3aa9de8411878805c122f90a11
+          path: .dependencies/base-cli
+
       - name: Set up Python
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065
         with:
@@ -33,6 +40,7 @@ jobs:
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip
+          python -m pip install --no-deps .dependencies/base-cli
           python -m pip install -r requirements-dev.txt
 
       - name: Run lightweight Base validation

.github/workflows/pylint.yml

@@ -25,7 +25,7 @@ jobs:
       - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5
         with:
           repository: basefoundry/base-cli
-          ref: fc3ac1826b62de9c84d40c77b131ea3c5e660f14
+          ref: 9f3ed25fc0991e3aa9de8411878805c122f90a11
           path: .dependencies/base-cli
 
       - name: Set up Python ${{ matrix.python-version }}
@@ -36,6 +36,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
+          python -m pip install --no-deps .dependencies/base-cli
           python -m pip install -r requirements-dev.txt
 
       - name: Run Pylint

.github/workflows/tests.yml

@@ -31,7 +31,7 @@ jobs:
       - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5
         with:
           repository: basefoundry/base-cli
-          ref: fc3ac1826b62de9c84d40c77b131ea3c5e660f14
+          ref: 9f3ed25fc0991e3aa9de8411878805c122f90a11
           path: .dependencies/base-cli
 
       - name: Set up Python
@@ -42,6 +42,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
+          python -m pip install --no-deps .dependencies/base-cli
           python -m pip install -r requirements-dev.txt
 
       - name: Run Python tests
@@ -72,7 +73,7 @@ jobs:
       - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5
         with:
           repository: basefoundry/base-cli
-          ref: fc3ac1826b62de9c84d40c77b131ea3c5e660f14
+          ref: 9f3ed25fc0991e3aa9de8411878805c122f90a11
           path: .dependencies/base-cli
 
       - name: Expose standalone Python package checkout as sibling
@@ -124,7 +125,7 @@ jobs:
       - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5
         with:
           repository: basefoundry/base-cli
-          ref: fc3ac1826b62de9c84d40c77b131ea3c5e660f14
+          ref: 9f3ed25fc0991e3aa9de8411878805c122f90a11
           path: .dependencies/base-cli
 
       - name: Expose standalone Python package checkout as sibling
@@ -216,7 +217,7 @@ jobs:
       - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5
         with:
           repository: basefoundry/base-cli
-          ref: fc3ac1826b62de9c84d40c77b131ea3c5e660f14
+          ref: 9f3ed25fc0991e3aa9de8411878805c122f90a11
           path: .dependencies/base-cli
 
       - name: Expose standalone Python package checkout as sibling
@@ -240,10 +241,12 @@ jobs:
         run: |
           python -m venv .integration-venv
           .integration-venv/bin/python -m pip install --upgrade pip
+          .integration-venv/bin/python -m pip install --no-deps .dependencies/base-cli
           .integration-venv/bin/python -m pip install -r requirements-dev.txt
           mkdir -p "$HOME/.base.d/base"
           python -m venv "$HOME/.base.d/base/.venv"
           "$HOME/.base.d/base/.venv/bin/python" -m pip install --upgrade pip
+          "$HOME/.base.d/base/.venv/bin/python" -m pip install --no-deps .dependencies/base-cli
           "$HOME/.base.d/base/.venv/bin/python" -m pip install -r requirements-dev.txt
           sudo apt-get update
           sudo apt-get install -y bats
@@ -278,7 +281,7 @@ jobs:
       - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5
         with:
           repository: basefoundry/base-cli
-          ref: fc3ac1826b62de9c84d40c77b131ea3c5e660f14
+          ref: 9f3ed25fc0991e3aa9de8411878805c122f90a11
           path: .dependencies/base-cli
 
       - name: Expose reusable Bash library checkout as sibling
@@ -317,6 +320,7 @@ jobs:
           mkdir -p "$HOME/.base.d/base"
           python3 -m venv "$HOME/.base.d/base/.venv"
           "$HOME/.base.d/base/.venv/bin/python" -m pip install --upgrade pip
+          "$HOME/.base.d/base/.venv/bin/python" -m pip install --no-deps .dependencies/base-cli
           "$HOME/.base.d/base/.venv/bin/python" -m pip install -r requirements-dev.txt
 
       - name: Run Ubuntu source-checkout validation
@@ -336,6 +340,12 @@ jobs:
     steps:
       - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5
 
+      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5
+        with:
+          repository: basefoundry/base-cli
+          ref: 9f3ed25fc0991e3aa9de8411878805c122f90a11
+          path: .dependencies/base-cli
+
       - name: Set up Python
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065
         with:
@@ -352,6 +362,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
+          python -m pip install --no-deps .dependencies/base-cli
           python -m pip install -r requirements-dev.txt
           sudo apt-get update
           sudo apt-get install -y shellcheck
@@ -362,7 +373,12 @@ jobs:
 
       - name: Run pip-audit
         run: |
-          python -m pip_audit --cache-dir "$RUNNER_TEMP/pip-audit" -r requirements-dev.txt
+          # Start from -r requirements-dev.txt, but omit base-cli because it
+          # is checked out locally and may not be published during review.
+          grep -Eiv '^base-cli[[:space:]]*=' requirements-dev.txt \
+            > "$RUNNER_TEMP/base-audit-requirements.txt"
+          python -m pip_audit --cache-dir "$RUNNER_TEMP/pip-audit" \
+            -r "$RUNNER_TEMP/base-audit-requirements.txt"
 
       - name: Run ShellCheck
         run: |

cli/python/base_cli_adapters/config.py

@@ -6,6 +6,7 @@
 from pathlib import Path
 from typing import Any
 
+from base_cli import ConfigurationError
 from base_cli.config import load_yaml_file as load_cli_yaml_file
 from base_setup.ide_schema import parse_ide_extensions
 from base_setup.ide_schema import parse_ide_settings
@@ -67,14 +68,17 @@ def read_user_config(
     *,
     supported_ides: frozenset[str] | None = SUPPORTED_IDES,
 ) -> UserConfig:
-    raw = load_user_config(home)
-    path = user_config_path(home)
-    return UserConfig(
-        raw=raw,
-        workspace=_read_user_workspace_config(path, raw.get("workspace")),
-        github=_read_user_github_config(path, raw.get("github")),
-        ide=_read_user_ide_config(path, raw.get("ide"), supported_ides=supported_ides),
-    )
+    try:
+        raw = load_user_config(home)
+        path = user_config_path(home)
+        return UserConfig(
+            raw=raw,
+            workspace=_read_user_workspace_config(path, raw.get("workspace")),
+            github=_read_user_github_config(path, raw.get("github")),
+            ide=_read_user_ide_config(path, raw.get("ide"), supported_ides=supported_ides),
+        )
+    except ValueError as exc:
+        raise ConfigurationError(str(exc)) from exc
 
 
 def _read_user_workspace_config(path: Path, workspace_data: Any) -> UserWorkspaceConfig:

cli/python/base_cli_adapters/runtime.py

@@ -2,7 +2,7 @@
 
 from pathlib import Path
 
-from base_cli._runtime import RuntimeLayout
+from base_cli.runtime import RuntimeLayout
 
 from .paths import runtime_owner_root
 from .paths import runtime_run_directory_name

cli/python/base_github_projects/project_parser.py

@@ -154,6 +154,9 @@ def parse_project_options(
             state.allow_cross_repo = True
             index += 1
             continue
+        if apply_inline_option(state, arg, allow_fields=allow_fields):
+            index += 1
+            continue
         consumed = apply_spaced_option(state, remaining, index, allow_fields=allow_fields)
         if consumed:
             index += consumed
@@ -183,6 +186,21 @@ def apply_spaced_option(state: OptionState, remaining: list[str], index: int, *,
     return OPTION_NOT_CONSUMED
 
 
+def apply_inline_option(state: OptionState, argument: str, *, allow_fields: bool) -> bool:
+    """Apply Click-compatible ``--option=value`` syntax to delegated options."""
+    if not argument.startswith("--") or "=" not in argument:
+        return False
+
+    option, value = argument.split("=", 1)
+    if option in PROJECT_VALUE_OPTIONS:
+        apply_project_option(state, option, value)
+        return True
+    if allow_fields and option in ISSUE_FIELD_OPTIONS:
+        state.field_values[option[2:]] = value
+        return True
+    return False
+
+
 def option_value(remaining: list[str], index: int) -> str:
     option = remaining[index]
     if index + 1 >= len(remaining):

cli/python/base_github_projects/tests/test_engine.py

@@ -26,19 +26,13 @@ def test_delegated_usage_uses_basectl_gh_project_prefix(
     assert "base_github_projects" not in captured.err
 
 
-def test_main_rejects_equals_form_project_options(
-    capsys: pytest.CaptureFixture[str],
-    monkeypatch: pytest.MonkeyPatch,
-    tmp_path: Path,
-) -> None:
-    monkeypatch.setenv("HOME", str(tmp_path))
-    monkeypatch.setenv("BASE_CACHE_DIR", str(tmp_path / ".cache" / "base"))
-
-    status = engine.main(["project", "configure", "--project=Base Roadmap", "--dry-run"])
+def test_parse_project_configure_accepts_equals_form_options() -> None:
+    args = engine.parse_args(
+        ("project", "configure", "--project=Base Roadmap", "--dry-run"),
+    )
 
-    captured = capsys.readouterr()
-    assert status == 2
-    assert "Option '--project' uses unsupported equals syntax." in captured.err
+    assert args.project_title == "Base Roadmap"
+    assert args.dry_run is True
 
 
 def test_parse_project_configure_arguments() -> None:

cli/python/base_history/tests/test_engine.py

@@ -109,6 +109,7 @@ def test_text_output_lists_recent_history_and_missing_log_marker(self) -> None:
             )
 
             status, stdout, stderr = invoke([], cache_root)
+            records = engine.recent_history(cache_root)
 
         self.assertEqual(status, 0)
         self.assertEqual(stderr, "")
@@ -117,7 +118,8 @@ def test_text_output_lists_recent_history_and_missing_log_marker(self) -> None:
         self.assertIn("PROJECT", stdout)
         self.assertIn("check", stdout)
         self.assertIn("error", stdout)
-        self.assertIn("missing", stdout)
+        self.assertEqual(len(records), 1)
+        self.assertTrue(engine.display_log_path(records[0]).endswith(" (missing)"))
 
     def test_text_table_expands_columns_for_long_command_and_project(self) -> None:
         with tempfile.TemporaryDirectory() as tmpdir:

cli/python/base_pr_policy/tests/test_engine.py

@@ -42,12 +42,15 @@ def test_explicit_manifest_populates_history_project_metadata(tmp_path) -> None:
     assert record["manifest"] == str(manifest_path.resolve())
 
 
-def test_main_rejects_equals_form_options(capsys) -> None:
+def test_main_accepts_equals_form_options(capsys, monkeypatch, tmp_path) -> None:
+    monkeypatch.setenv("HOME", str(tmp_path))
+    monkeypatch.setenv("BASE_CACHE_DIR", str(tmp_path / ".cache" / "base"))
+
     status = engine.main(["body", "--issue=403"])
 
     captured = capsys.readouterr()
-    assert status == 2
-    assert "Option '--issue' uses unsupported equals syntax." in captured.err
+    assert status == 0
+    assert "Fixes #403" in captured.out
 
 
 def test_render_pr_body_uses_default_label_and_path_sections() -> None:

cli/python/base_projects/tests/test_engine.py

@@ -383,7 +383,7 @@ def test_main_reports_config_errors_without_traceback(self) -> None:
             user_config="workspace: [not-a-mapping]\n",
         )
 
-        self.assertEqual(status, 1)
+        self.assertEqual(status, 2)
         self.assertIn("workspace must be a mapping", stderr)
         self.assertNotIn("Traceback", stderr)
 

cli/python/base_trust/tests/test_engine.py

@@ -120,7 +120,7 @@ def test_require_explicit_manifest_populates_history_project_metadata(self) -> N
                     env={"BASE_HOME": str(root / "base")},
                 )
 
-            self.assertEqual(result.exit_code, 0)
+            self.assertEqual(result.exit_code, 1)
             self.assertIn("Manifest-declared commands are not allowed", result.stderr)
             self.assertEqual(len(captured), 1)
             record = build_finished_record(*captured[0])

docs/base-cli.md

@@ -99,9 +99,9 @@ if __name__ == "__main__":
 
 The command function receives `ctx` as its first argument. Infrastructure is
 created immediately before command execution and cleaned up afterward.
-`base_cli.run_app()` applies Base's command syntax guard before Click parses
-arguments: long options with values must use space-separated syntax, such as
-`--name Ada`; equals-form values such as `--name=Ada` are rejected.
+`base_cli.run_app()` preserves Click's native option syntax, including both
+space-separated values such as `--name Ada` and equals-form values such as
+`--name=Ada`.
 
 ## Package Layout
 
@@ -141,7 +141,6 @@ registration.
 ```python
 ctx.cli_name       # str
 ctx.run_id         # str
-ctx.base_home      # Path | None
 ctx.application_home  # Path | None; neutral application-home alias
 ctx.project_name   # selected project name, or None
 ctx.project_root   # Path | None
@@ -157,14 +156,20 @@ ctx.log_dir        # run_root/logs
 ctx.cache_dir      # owner_root/cache/components/<cli-name>
 ctx.temp_dir       # run_root/tmp/<cli-name>/<run-id>
 ctx.log_file       # run_root/logs/primary.log, or None when disabled
-ctx.config         # dict
+ctx.config         # consumer-owned configuration payload
+ctx.framework_config # validated framework lifecycle settings, or None
+ctx.config_provenance # configuration source mapping, when provided
 ctx.user_config    # typed user config from ~/.base.d/config.yaml
+ctx.application_context # optional consumer application state
+ctx.services        # optional consumer services
 ctx.history_display_command  # consumer policy for persisted command labels
 ctx.environment    # str
 ctx.debug          # bool
 ctx.dry_run        # bool
 ctx.keep_temp      # bool
 ctx.quiet          # bool
+ctx.json_output    # bool
+ctx.rich           # bool; optional Rich integration enabled
 ctx.log            # logging.Logger
 ```
 
@@ -368,9 +373,8 @@ Direct `base_cli.App` command packages get:
 | `--version` | show the CLI version when configured |
 | `--help` | Click help |
 
-Long option values must use the space-separated form, for example
-`--environment prod`. Base rejects `--option=value` before Click parses
-arguments.
+Long option values accept either Click form, for example `--environment prod`
+or `--environment=prod`.
 
 These are direct Python package options. Public `basectl` launchers expose
 `-v` for command-level debug logs and command-specific flags from

requirements-dev.txt

@@ -1,6 +1,6 @@
 pylint==3.3.9
 click==8.4.1
-base-cli==0.2.0
+base-cli==0.4.0
 PyYAML==6.0.3
 pytest==9.0.3
 pytest-cov==7.1.0