refactor: improve brew cleanup timeout handling and remove app_caches, clean_extras, and optimize_core tests.

tests/core_timeout.bats

@@ -0,0 +1,188 @@
+#!/usr/bin/env bats
+
+setup() {
+    PROJECT_ROOT="$(cd "${BATS_TEST_DIRNAME}/.." && pwd)"
+    export PROJECT_ROOT
+    export MO_DEBUG=0
+}
+
+@test "run_with_timeout: command completes before timeout" {
+    result=$(bash -c "
+        set -euo pipefail
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout 5 echo 'success'
+    ")
+    [[ "$result" == "success" ]]
+}
+
+@test "run_with_timeout: zero timeout runs command normally" {
+    result=$(bash -c "
+        set -euo pipefail
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout 0 echo 'no_timeout'
+    ")
+    [[ "$result" == "no_timeout" ]]
+}
+
+@test "run_with_timeout: invalid timeout runs command normally" {
+    result=$(bash -c "
+        set -euo pipefail
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout invalid echo 'no_timeout'
+    ")
+    [[ "$result" == "no_timeout" ]]
+}
+
+@test "run_with_timeout: negative timeout runs command normally" {
+    result=$(bash -c "
+        set -euo pipefail
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout -5 echo 'no_timeout'
+    ")
+    [[ "$result" == "no_timeout" ]]
+}
+
+@test "run_with_timeout: preserves command exit code on success" {
+    bash -c "
+        set -euo pipefail
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout 5 true
+    "
+    exit_code=$?
+    [[ $exit_code -eq 0 ]]
+}
+
+@test "run_with_timeout: preserves command exit code on failure" {
+    set +e
+    bash -c "
+        set +e
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout 5 false
+        exit \$?
+    "
+    exit_code=$?
+    set -e
+    [[ $exit_code -eq 1 ]]
+}
+
+@test "run_with_timeout: returns 124 on timeout (if using gtimeout)" {
+    if ! command -v gtimeout >/dev/null 2>&1 && ! command -v timeout >/dev/null 2>&1; then
+        skip "gtimeout/timeout not available"
+    fi
+
+    set +e
+    bash -c "
+        set +e
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout 1 sleep 10
+        exit \$?
+    "
+    exit_code=$?
+    set -e
+    [[ $exit_code -eq 124 ]]
+}
+
+@test "run_with_timeout: kills long-running command" {
+    start_time=$(date +%s)
+    set +e
+    bash -c "
+        set +e
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout 2 sleep 30
+    " >/dev/null 2>&1
+    set -e
+    end_time=$(date +%s)
+    duration=$((end_time - start_time))
+
+    [[ $duration -lt 10 ]]
+}
+
+@test "run_with_timeout: handles fast-completing commands" {
+    start_time=$(date +%s)
+    bash -c "
+        set -euo pipefail
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout 10 echo 'fast'
+    " >/dev/null 2>&1
+    end_time=$(date +%s)
+    duration=$((end_time - start_time))
+
+    [[ $duration -lt 3 ]]
+}
+
+@test "run_with_timeout: works in pipefail mode" {
+    result=$(bash -c "
+        set -euo pipefail
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout 5 echo 'pipefail_test'
+    ")
+    [[ "$result" == "pipefail_test" ]]
+}
+
+@test "run_with_timeout: doesn't cause unintended exits" {
+    result=$(bash -c "
+        set -euo pipefail
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout 5 true || true
+        echo 'survived'
+    ")
+    [[ "$result" == "survived" ]]
+}
+
+@test "run_with_timeout: handles commands with arguments" {
+    result=$(bash -c "
+        set -euo pipefail
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout 5 echo 'arg1' 'arg2' 'arg3'
+    ")
+    [[ "$result" == "arg1 arg2 arg3" ]]
+}
+
+@test "run_with_timeout: handles commands with spaces in arguments" {
+    result=$(bash -c "
+        set -euo pipefail
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout 5 echo 'hello world'
+    ")
+    [[ "$result" == "hello world" ]]
+}
+
+@test "run_with_timeout: debug logging when MO_DEBUG=1" {
+    output=$(bash -c "
+        set -euo pipefail
+        export MO_DEBUG=1
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout 5 echo 'test' 2>&1
+    ")
+    [[ "$output" =~ TIMEOUT ]]
+}
+
+@test "run_with_timeout: no debug logging when MO_DEBUG=0" {
+    output=$(bash -c "
+        set -euo pipefail
+        export MO_DEBUG=0
+        unset MO_TIMEOUT_INITIALIZED
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        run_with_timeout 5 echo 'test'
+    " 2>/dev/null)
+    [[ "$output" == "test" ]]
+}
+
+@test "timeout.sh: prevents multiple sourcing" {
+    result=$(bash -c "
+        set -euo pipefail
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        echo 'loaded'
+    ")
+    [[ "$result" == "loaded" ]]
+}
+
+@test "timeout.sh: sets MOLE_TIMEOUT_LOADED flag" {
+    result=$(bash -c "
+        set -euo pipefail
+        source '$PROJECT_ROOT/lib/core/timeout.sh'
+        echo \"\$MOLE_TIMEOUT_LOADED\"
+    ")
+    [[ "$result" == "1" ]]
+}