Fix Claude-reported Base issues

CHANGELOG.md

@@ -27,6 +27,15 @@ and Base versions are tracked in the repo-root `VERSION` file.
 - Expanded `basectl repo init` to seed portable project Git workflow guidance
   and a standard pull request template for Base-managed repositories.
 
+### Fixed
+
+- Removed a hardcoded issue number from the 1.0 Homebrew upgrade reminder in
+  `basectl release`.
+- Kept `basectl ci setup --format json` output focused on a clean setup summary
+  instead of embedding the delegated setup log stream.
+- Validated workspace manifest repo URLs when a `repos[].url` value is provided.
+- Removed forbidden shell strict mode from the project installer template.
+
 ## [0.3.0] - 2026-06-06
 
 ### Added

CLAUDE.md

@@ -331,7 +331,7 @@ Machine-local user configuration managed by Base. Not edited by hand.
 User-managed simple preferences (e.g. `BASE_DEBUG=1`). Must not contain
 `BASE_HOME`, `BASE_BIN_DIR`, or other Base-owned runtime variables.
 
-### Runtime Variables Set by `base_init.sh`
+### Runtime Variables and CI Marker
 
 | Variable | Description |
 |----------|-------------|
@@ -342,6 +342,7 @@ User-managed simple preferences (e.g. `BASE_DEBUG=1`). Must not contain
 | `BASE_OS` | `macos` or `linux` |
 | `BASE_HOST` | Hostname |
 | `BASE_SHELL` | `bash` or `zsh` |
+| `BASE_CI` | Set to `true` by `basectl ci`, not `base_init.sh`, to signal non-interactive CI execution to setup and diagnostic commands |
 
 ---
 

cli/bash/commands/basectl/subcommands/ci.sh

@@ -26,6 +26,7 @@ Options:
 
 Purpose:
   Run Base setup, checks, and diagnostics in a non-interactive CI environment.
+  Sets BASE_CI=true so setup and diagnostic paths can choose CI-safe behavior.
 EOF
 }
 
@@ -179,19 +180,66 @@ base_ci_print_setup_json() {
     printf '}\n'
 }
 
-base_ci_run_setup() {
-    local args=()
+base_ci_compact_setup_output() {
+    local output_file="$1"
+    local line
+    local message=""
+
+    [[ -f "$output_file" ]] || return 0
+    while IFS= read -r line || [[ -n "$line" ]]; do
+        [[ -n "$line" ]] || continue
+        if [[ "$line" =~ ^[0-9]{4}-[0-9]{2}-[0-9]{2}[[:space:]][0-9]{2}:[0-9]{2}:[0-9]{2}[[:space:]][A-Z]+[[:space:]]+[^[:space:]]+[[:space:]]+(.*)$ ]]; then
+            message="${BASH_REMATCH[1]}"
+        else
+            message="$line"
+        fi
+    done < "$output_file"
+
+    printf '%s\n' "$message"
+}
+
+base_ci_run_setup_json() {
+    local args=("$@")
+    local stdout_file
+    local stderr_file
     local command_output
     local exit_code
 
+    stdout_file="$(mktemp "${TMPDIR:-/tmp}/base-ci-setup-stdout.XXXXXX")" || return 1
+    stderr_file="$(mktemp "${TMPDIR:-/tmp}/base-ci-setup-stderr.XXXXXX")" || {
+        rm -f "$stdout_file"
+        return 1
+    }
+
+    base_setup_subcommand_main "${args[@]}" > "$stdout_file" 2> "$stderr_file"
+    exit_code=$?
+
+    if [[ -s "$stdout_file" ]]; then
+        cat "$stdout_file" >&2
+    fi
+    if [[ -s "$stderr_file" ]]; then
+        cat "$stderr_file" >&2
+    fi
+
+    command_output="$(base_ci_compact_setup_output "$stderr_file")"
+    if [[ -z "$command_output" ]]; then
+        command_output="$(base_ci_compact_setup_output "$stdout_file")"
+    fi
+
+    rm -f "$stdout_file" "$stderr_file"
+    base_ci_print_setup_json "$command_output" "$exit_code"
+    return "$exit_code"
+}
+
+base_ci_run_setup() {
+    local args=()
+
     mapfile -t args < <(base_ci_setup_delegate_args)
     base_ci_source_subcommand_module setup || return 1
 
     if [[ "$BASE_CI_FORMAT" == json ]]; then
-        command_output="$(base_setup_subcommand_main "${args[@]}" 2>&1)"
-        exit_code=$?
-        base_ci_print_setup_json "$command_output" "$exit_code"
-        return "$exit_code"
+        base_ci_run_setup_json "${args[@]}"
+        return $?
     fi
 
     base_setup_subcommand_main "${args[@]}"

cli/bash/commands/basectl/tests/ci.bats

@@ -40,6 +40,7 @@ prepare_ci_runtime() {
     [[ "$output" == *"basectl ci check <project>"* ]]
     [[ "$output" == *"basectl ci doctor <project>"* ]]
     [[ "$output" == *"--format <text|json>"* ]]
+    [[ "$output" == *"BASE_CI=true"* ]]
 }
 
 @test "basectl ci requires a command and project" {
@@ -90,6 +91,27 @@ prepare_ci_runtime() {
     [ ! -f "$TEST_STATE_DIR/osascript-args" ]
 }
 
+@test "basectl ci setup json output summarizes stderr without embedding log stream" {
+    local workspace="$TEST_TMPDIR/workspace"
+
+    prepare_ci_runtime "$workspace"
+    printf '%s\n' \
+        "2026-06-10 10:15:32 INFO    setup_common.sh:122 Homebrew is already installed." \
+        "2026-06-10 10:15:33 ERROR   setup_common.sh:801 Python project setup layer failed." \
+        > "$TEST_STATE_DIR/project-setup-stderr"
+    printf '%s\n' 17 > "$TEST_STATE_DIR/project-setup-exit-code"
+
+    run_base_command_separate_stderr BASE_SETUP_TEST_WORKSPACE="$workspace" ci setup demo --format json
+
+    [ "$status" -eq 17 ]
+    [[ "$output" == *'"schema_version": 1'* ]]
+    [[ "$output" == *'"status": "error"'* ]]
+    [[ "$output" == *'"output": "Python project setup layer failed."'* ]]
+    [[ "$output" != *"setup_common.sh"* ]]
+    [[ "$stderr" == *"Homebrew is already installed."* ]]
+    [[ "$stderr" == *"Python project setup layer failed."* ]]
+}
+
 @test "basectl ci check supports Linux runtime-only JSON checks" {
     create_system_python3_stub
     create_project_setup_venv_stub "$TEST_HOME/.base.d/base/.venv"

cli/bash/commands/basectl/tests/repo.bats

@@ -22,6 +22,9 @@ load ./basectl_helpers.bash
     [[ "$output" == *'PROJECT_NAME="${PROJECT_NAME:-example-project}"'* ]]
     [[ "$output" == *'PROJECT_REPO_URL="${PROJECT_REPO_URL:-https://github.com/example/example-project.git}"'* ]]
     [[ "$output" == *'basectl" setup --manifest "$PROJECT_DIR/base_manifest.yaml" "$PROJECT_NAME"'* ]]
+    [[ "$output" == *"Explicit error handling is used instead of set -e"* ]]
+    [[ "$output" == *'run git -C "$BASE_DIR" pull --ff-only || die'* ]]
+    [[ "$output" != *"set -euo pipefail"* ]]
 }
 
 @test "basectl repo installer-template writes an executable template" {

cli/bash/commands/basectl/tests/setup_helpers.bash

@@ -434,6 +434,37 @@ run_base_command() {
         "$BASE_REPO_ROOT/bin/basectl" "${command_args[@]}"
 }
 
+run_base_command_separate_stderr() {
+    local arg
+    local env_args=()
+    local command_args=()
+    local python_prefix="$TEST_TMPDIR/python-prefix"
+    local xcode_dir="$TEST_TMPDIR/CommandLineTools"
+
+    for arg in "$@"; do
+        if [[ ${#command_args[@]} -eq 0 && "$arg" == *=* ]]; then
+            env_args+=("$arg")
+        else
+            command_args+=("$arg")
+        fi
+    done
+
+    run --separate-stderr env \
+        HOME="$TEST_HOME" \
+        PATH="$TEST_MOCKBIN:$TEST_BASH_BIN_DIR:/usr/bin:/bin:/usr/sbin:/sbin" \
+        OSTYPE="${OSTYPE_OVERRIDE:-darwin24}" \
+        BASE_TEST_MODE=true \
+        BASE_SETUP_BREW_BIN="$TEST_MOCKBIN/brew" \
+        BASE_SETUP_TEST_STATE_DIR="$TEST_STATE_DIR" \
+        BASE_SETUP_TEST_MOCKBIN="$TEST_MOCKBIN" \
+        BASE_SETUP_TEST_PYTHON_PREFIX="$python_prefix" \
+        BASE_SETUP_XCODE_COMMAND_LINE_TOOLS_DIR="$xcode_dir" \
+        BASE_SETUP_XCODE_WAIT_TIMEOUT_SECONDS=5 \
+        BASE_SETUP_XCODE_WAIT_INTERVAL_SECONDS=0 \
+        "${env_args[@]}" \
+        "$BASE_REPO_ROOT/bin/basectl" "${command_args[@]}"
+}
+
 create_base_venv_stub() {
     local venv_dir="${1:-$TEST_HOME/.base.d/base/.venv}"
 
@@ -544,6 +575,9 @@ if [[ "${1:-}" == "-m" && "${2:-}" == "base_setup" ]]; then
     elif [[ "$action" == "doctor" ]]; then
         printf 'ok     demo-artifact               Project artifact check passed.\n'
     fi
+    if [[ -f "$BASE_SETUP_TEST_STATE_DIR/project-setup-stderr" ]]; then
+        cat "$BASE_SETUP_TEST_STATE_DIR/project-setup-stderr" >&2
+    fi
     exit "$(cat "$BASE_SETUP_TEST_STATE_DIR/project-setup-exit-code")"
 fi
 if [[ "${1:-}" == "-m" && "${2:-}" == "base_projects" && "${3:-}" == "resolve" ]]; then

cli/python/base_projects/tests/test_workspace_manifest.py

@@ -42,6 +42,62 @@ def test_reads_workspace_manifest_with_defaults(self) -> None:
         self.assertFalse(manifest.repos[1].required)
         self.assertIsNone(manifest.repos[1].url)
 
+    def test_accepts_common_git_url_forms(self) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            root = Path(tmpdir)
+            path = root / "workspace.yaml"
+            local_repo = root / "local-repo"
+            write_workspace_manifest(
+                path,
+                f"""
+schema_version: 1
+workspace:
+  name: demo-workspace
+repos:
+  - name: https-repo
+    url: https://github.com/codeforester/base.git
+  - name: ssh-repo
+    url: ssh://git@github.com/codeforester/base.git
+  - name: scp-repo
+    url: git@github.com:codeforester/base.git
+  - name: local-repo
+    url: {local_repo}
+""",
+            )
+
+            manifest = read_workspace_manifest(path)
+
+        self.assertEqual(
+            [repo.url for repo in manifest.repos],
+            [
+                "https://github.com/codeforester/base.git",
+                "ssh://git@github.com/codeforester/base.git",
+                "git@github.com:codeforester/base.git",
+                str(local_repo),
+            ],
+        )
+
+    def test_rejects_repo_url_without_git_url_form(self) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            path = Path(tmpdir) / "workspace.yaml"
+            write_workspace_manifest(
+                path,
+                """
+schema_version: 1
+workspace:
+  name: demo-workspace
+repos:
+  - name: base
+    url: github.com/codeforester/base.git
+""",
+            )
+
+            with self.assertRaisesRegex(
+                WorkspaceManifestError,
+                "repos\\[1\\]\\.url does not look like a Git URL or local path",
+            ):
+                read_workspace_manifest(path)
+
     def test_requires_schema_version(self) -> None:
         with tempfile.TemporaryDirectory() as tmpdir:
             path = Path(tmpdir) / "workspace.yaml"

cli/python/base_projects/workspace_manifest.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import re
 from dataclasses import dataclass
 from pathlib import Path
 from typing import Any
@@ -124,6 +125,8 @@ def _read_repo(path: Path, index: int, repo_data: Any) -> WorkspaceManifestRepo:
 
     name = _read_repo_name(path, index, repo_data.get("name"))
     url = _read_optional_string(path, f"repos[{index}].url", repo_data.get("url"))
+    if url is not None:
+        _validate_repo_url(path, index, url)
     default_branch = _read_optional_string(
         path,
         f"repos[{index}].default_branch",
@@ -157,6 +160,18 @@ def _read_optional_string(path: Path, field: str, value: Any) -> str | None:
     return value.strip()
 
 
+def _validate_repo_url(path: Path, index: int, url: str) -> None:
+    if url.startswith(("https://", "http://", "git://", "ssh://", "file://")):
+        return
+    if re.match(r"^[^@\s]+@[^:\s]+:.+$", url):
+        return
+    if Path(url).is_absolute():
+        return
+    raise WorkspaceManifestError(
+        f"{path}: repos[{index}].url does not look like a Git URL or local path: '{url}'."
+    )
+
+
 def _read_required(path: Path, index: int, required_data: Any) -> bool:
     if required_data is None:
         return True

cli/python/base_release/engine.py

@@ -602,7 +602,7 @@ def homebrew_handoff_lines(ctx: ReleaseContext, *, after_publish: bool) -> tuple
         f"    brew upgrade {homebrew.package}",
     ]
     if requires_homebrew_upgrade_rehearsal(ctx.version):
-        lines.append("  1.0 reminder: complete the Homebrew upgrade rehearsal tracked by #526.")
+        lines.append("  1.0 reminder: validate the Homebrew upgrade path before publishing.")
     return tuple(lines)
 
 

cli/python/base_release/tests/test_engine.py

@@ -167,6 +167,34 @@ def test_plan_prints_github_and_homebrew_handoff(self) -> None:
         self.assertIn("brew upgrade codeforester/demo/demo", stdout)
 
 
+    def test_plan_prints_1_0_homebrew_upgrade_reminder_without_issue_number(self) -> None:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            root = Path(tmpdir)
+            changelog = "\n".join(
+                [
+                    "# Changelog",
+                    "",
+                    "## [1.0.0] - 2026-06-10",
+                    "",
+                    "- Stable release.",
+                ]
+            )
+            manifest_path = write_release_project(
+                root,
+                version_file_content="1.0.0\n",
+                changelog=changelog,
+            )
+
+            status, stdout, stderr = run_engine(
+                ["plan", "--version", "1.0.0", "--manifest", str(manifest_path)],
+                root,
+            )
+
+        self.assertEqual(status, 0, stderr)
+        self.assertIn("1.0 reminder: validate the Homebrew upgrade path before publishing.", stdout)
+        self.assertNotIn("#526", stdout)
+
+
     def test_plan_prints_no_homebrew_handoff_for_github_only_project(self) -> None:
         with tempfile.TemporaryDirectory() as tmpdir:
             root = Path(tmpdir)

docs/basectl-ci.md

@@ -38,6 +38,11 @@ without prompting, `basectl ci` fails with a clear fix message.
 - run project artifact setup through the same manifest path as `basectl setup`
 - emit a small JSON wrapper when `--format json` is requested
 
+`BASE_CI=true` is the Base-specific CI marker. Setup and diagnostic code use it
+to select non-interactive, CI-safe behavior, including the runtime-only Linux
+path that can allow system Python when Homebrew bootstrap is not available.
+`CI=true` is also set for compatibility with common CI-aware tools.
+
 `basectl ci check <project>` should:
 
 - run read-only Base and project checks

docs/runtime-environment.md

@@ -74,6 +74,17 @@ explicit Bash script, or starts a Base runtime Bash shell.
 | `BASE_HOST` | Base | Short host name from `hostname -s`. Used by runtime metadata and prompts. | Do not set. Readonly after `base_init.sh`. |
 | `BASE_SHELL` | Base | Legacy runtime marker. Plain `base_init.sh` defaults it to `bash`; Base runtime shells seed it as `1` before `base_init.sh`. New code should avoid adding new meanings to it. | Do not set in user config. Readonly after `base_init.sh`. |
 
+## CI Runtime Variables
+
+`basectl ci` sets these variables while delegating to setup, check, and doctor
+paths. They are scoped to that command invocation and are not part of the
+readonly `base_init.sh` runtime contract.
+
+| Variable | Owner | Meaning and impact | User changes |
+| --- | --- | --- | --- |
+| `BASE_CI` | Base | Set to `true` by `basectl ci` so Base setup and diagnostics can choose non-interactive CI-safe behavior, including the runtime-only Linux system-Python fallback gate. | Do not set directly; use `basectl ci`. |
+| `CI` | Base/tooling convention | Set to `true` by `basectl ci` for compatibility with common CI-aware tools. | CI systems may already set this. Base sets it for delegated commands when using `basectl ci`. |
+
 ## Command Dispatch Variables
 
 `bin/basectl` sets these before sourcing the selected Bash command or explicit