fix(config): honor --config across internal reloads and multi-file merges

cmd/config/operations.go

@@ -7,28 +7,46 @@ import (
 	cfg "github.com/cloudposse/atmos/pkg/config"
 	"github.com/cloudposse/atmos/pkg/data"
 	"github.com/cloudposse/atmos/pkg/perf"
+	"github.com/cloudposse/atmos/pkg/schema"
 	"github.com/cloudposse/atmos/pkg/ui"
+	u "github.com/cloudposse/atmos/pkg/utils"
 	atmosyaml "github.com/cloudposse/atmos/pkg/yaml"
 )
 
 // valueType holds the --type flag for `config set`.
 var valueType string
 
 var configGetCmd = &cobra.Command{
-	Use:     "get <path>",
-	Short:   "Read a value from atmos.yaml by dot-notation path",
-	Long:    "Read a value from atmos.yaml using a dot-notation path (e.g. logs.level).",
+	Use:   "get <path>",
+	Short: "Read a value from the effective Atmos configuration by dot-notation path",
+	Long: `Read a value using a dot-notation path (e.g. logs.level) from the effective,
+fully-merged Atmos configuration for this invocation -- the same configuration
+"terraform plan", "list stacks", etc. actually use, including every --config
+file, --config-path directory, and profile applied on top of each other. This
+can differ from what a single physical atmos.yaml file declares on its own
+(cloudposse/atmos#2867): use "atmos config format" or read the file directly
+to inspect one file's own declared value instead.`,
 	Example: "atmos config get logs.level",
 	Args:    cobra.ExactArgs(1),
 	RunE: func(cmd *cobra.Command, args []string) error {
 		defer perf.Track(atmosConfigPtr, "config.getRunE")()
 
-		file, err := resolveConfigFile(cmd)
+		// Reload rather than reuse atmosConfigPtr, mirroring configListCmd: this keeps `get`
+		// independently correct (and independently testable via RunE) even before root.go's
+		// PersistentPreRun has populated the package-level pointer. Safe to call with an empty
+		// ConfigAndStacksInfo{} -- LoadConfig now falls back to os.Args/env for
+		// --config/--config-path/--base-path itself (cloudposse/atmos#2868).
+		atmosConfig, err := cfg.InitCliConfig(schema.ConfigAndStacksInfo{}, false)
+		if err != nil {
+			return err
+		}
+
+		effectiveYAML, err := u.ConvertToYAML(atmosConfig)
 		if err != nil {
 			return err
 		}
 
-		value, err := atmosyaml.GetFile(file, args[0])
+		value, err := atmosyaml.Get([]byte(effectiveYAML), args[0])
 		if err != nil {
 			return err
 		}

cmd/config/operations_test.go

@@ -1,15 +1,21 @@
 package config
 
 import (
+	"bytes"
+	stdio "io"
 	"os"
 	"path/filepath"
+	"strings"
 	"testing"
 
 	"github.com/spf13/cobra"
+	"github.com/spf13/viper"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 
 	errUtils "github.com/cloudposse/atmos/errors"
+	"github.com/cloudposse/atmos/pkg/data"
+	iolib "github.com/cloudposse/atmos/pkg/io"
 	"github.com/cloudposse/atmos/pkg/schema"
 	atmosyaml "github.com/cloudposse/atmos/pkg/yaml"
 )
@@ -146,6 +152,66 @@ func TestConfigGetCommand_MissingValue(t *testing.T) {
 	require.ErrorIs(t, err, atmosyaml.ErrYAMLPathNotFound)
 }
 
+// configGetTestStreams is a minimal io.Streams implementation for capturing data output,
+// mirroring configSchemaTestStreams in schema_test.go.
+type configGetTestStreams struct {
+	stdin  stdio.Reader
+	stdout *bytes.Buffer
+	stderr *bytes.Buffer
+}
+
+func (ts *configGetTestStreams) Input() stdio.Reader     { return ts.stdin }
+func (ts *configGetTestStreams) Output() stdio.Writer    { return ts.stdout }
+func (ts *configGetTestStreams) Error() stdio.Writer     { return ts.stderr }
+func (ts *configGetTestStreams) RawOutput() stdio.Writer { return ts.stdout }
+func (ts *configGetTestStreams) RawError() stdio.Writer  { return ts.stderr }
+
+// TestConfigGetCommand_ReportsEffectiveMergedValue reproduces the "stale value" half of
+// cloudposse/atmos#2867: `atmos config get` used to read only the FIRST --config file
+// directly off disk (resolveConfigFile picked cfgFiles[0]), so a second --config file's
+// override was invisible to `get` even though the rest of atmos (stack discovery, etc.)
+// correctly used the merged value. `get` must report the same effective value everything
+// else uses.
+func TestConfigGetCommand_ReportsEffectiveMergedValue(t *testing.T) {
+	dir := t.TempDir()
+	mainFile := filepath.Join(dir, "main.yaml")
+	fragmentFile := filepath.Join(dir, "fragment.yaml")
+
+	require.NoError(t, os.WriteFile(mainFile, []byte(`
+base_path: "."
+stacks:
+  base_path: "stacks"
+  included_paths:
+    - "deploy/**/*"
+`), 0o644))
+	require.NoError(t, os.WriteFile(fragmentFile, []byte(`
+stacks:
+  included_paths:
+    - "deploy/**/*"
+    - "other/**/*"
+`), 0o644))
+
+	streams := &configGetTestStreams{stdin: &bytes.Buffer{}, stdout: &bytes.Buffer{}, stderr: &bytes.Buffer{}}
+	ioCtx, err := iolib.NewContext(iolib.WithStreams(streams))
+	require.NoError(t, err)
+	data.InitWriter(ioCtx)
+	t.Cleanup(data.Reset)
+
+	viper.Reset()
+	t.Cleanup(viper.Reset)
+
+	origArgs := os.Args
+	t.Cleanup(func() { os.Args = origArgs })
+	os.Args = []string{"atmos", "--config", mainFile + "," + fragmentFile, "config", "get", "stacks.included_paths"}
+
+	require.NoError(t, configGetCmd.RunE(configGetCmd, []string{"stacks.included_paths"}))
+
+	output := streams.stdout.String()
+	assert.True(t, strings.Contains(output, "deploy/**/*"), "output should contain the first file's value: %s", output)
+	assert.True(t, strings.Contains(output, "other/**/*"),
+		"output must reflect the SECOND --config file's override, not just the first file's stale value: %s", output)
+}
+
 func TestConfigSetCommand_TypeVariants(t *testing.T) {
 	dir := t.TempDir()
 	file := filepath.Join(dir, "atmos.yaml")

internal/exec/describe_workflows_test.go

@@ -87,6 +87,11 @@ workflows:
 	// Update config with the correct base path
 	config.BasePath = tmpDir
 	config.Workflows.BasePath = "stacks/workflows"
+	// Refresh derived absolute paths (e.g. WorkflowsDirAbsolutePath) after mutating BasePath
+	// directly -- real callers only ever get a fresh AtmosConfiguration from InitCliConfig,
+	// which computes these together; a manual post-load field mutation must recompute them
+	// too or ExecuteDescribeWorkflows would resolve against the stale pre-mutation paths.
+	require.NoError(t, cfg.AtmosConfigAbsolutePaths(&config))
 
 	tests := []struct {
 		name          string
@@ -190,6 +195,7 @@ workflows:
 	config := initTestConfig(t)
 	config.BasePath = tmpDir
 	config.Workflows.BasePath = "stacks/workflows"
+	require.NoError(t, cfg.AtmosConfigAbsolutePaths(&config))
 
 	tests := []struct {
 		name              string
@@ -287,6 +293,7 @@ workflows:
 	config := initTestConfig(t)
 	config.BasePath = tmpDir
 	config.Workflows.BasePath = "stacks/workflows"
+	require.NoError(t, cfg.AtmosConfigAbsolutePaths(&config))
 
 	// Should continue processing and return valid workflows despite invalid file.
 	listResult, _, _, err := ExecuteDescribeWorkflows(config)
@@ -326,6 +333,7 @@ some_other_key:
 	config := initTestConfig(t)
 	config.BasePath = tmpDir
 	config.Workflows.BasePath = "stacks/workflows"
+	require.NoError(t, cfg.AtmosConfigAbsolutePaths(&config))
 
 	// Should continue processing and return valid workflows.
 	listResult, _, _, err := ExecuteDescribeWorkflows(config)
@@ -344,6 +352,7 @@ func TestExecuteDescribeWorkflows_EmptyWorkflowsDirectory(t *testing.T) {
 	config := initTestConfig(t)
 	config.BasePath = tmpDir
 	config.Workflows.BasePath = "stacks/workflows"
+	require.NoError(t, cfg.AtmosConfigAbsolutePaths(&config))
 
 	// Empty workflows directory.
 	listResult, mapResult, allResult, err := ExecuteDescribeWorkflows(config)

internal/exec/validate_component.go

@@ -30,6 +30,20 @@ func getBasePathToUse(atmosConfig *schema.AtmosConfiguration) string {
 	return atmosConfig.BasePath
 }
 
+// getWorkflowsDirToUse returns the appropriate workflows directory for file resolution. It
+// prefers the precomputed WorkflowsDirAbsolutePath (set by AtmosConfigAbsolutePaths, the same
+// mechanism cloudposse/atmos#2864 uses for the top-level base_path), falling back to joining
+// the raw BasePath/Workflows.BasePath for callers that construct an AtmosConfiguration by hand
+// without running it through AtmosConfigAbsolutePaths first (e.g. tests).
+func getWorkflowsDirToUse(atmosConfig *schema.AtmosConfiguration) string {
+	if atmosConfig.WorkflowsDirAbsolutePath != "" {
+		return atmosConfig.WorkflowsDirAbsolutePath
+	}
+	// u.JoinPath (unlike filepath.Join) returns an already-absolute Workflows.BasePath as-is
+	// instead of nesting it under BasePath.
+	return u.JoinPath(atmosConfig.BasePath, atmosConfig.Workflows.BasePath)
+}
+
 // enableProvenanceForRichOutput sets atmosConfig.TrackProvenance when the
 // resolved output format is "rich". Provenance is enabled only for the rich
 // invocation: it lets the command map JSON Schema fields back to the

internal/exec/vendor_utils.go

@@ -130,19 +130,34 @@ func ReadAndProcessVendorConfigFile(
 	return vendorConfig, true, foundVendorConfigFile, nil
 }
 
+// getVendorDirToUse returns the appropriate vendor directory for file resolution. It prefers
+// the precomputed VendorDirAbsolutePath (set by AtmosConfigAbsolutePaths, the same mechanism
+// cloudposse/atmos#2864 uses for the top-level base_path), falling back to joining the raw
+// BasePath/Vendor.BasePath for callers that construct an AtmosConfiguration by hand without
+// running it through AtmosConfigAbsolutePaths first (e.g. tests). Mirrors getWorkflowsDirToUse
+// and getBasePathToUse (validate_component.go).
+func getVendorDirToUse(atmosConfig *schema.AtmosConfiguration) string {
+	if atmosConfig.VendorDirAbsolutePath != "" {
+		return atmosConfig.VendorDirAbsolutePath
+	}
+	// u.JoinPath (unlike filepath.Join) returns an already-absolute Vendor.BasePath as-is
+	// instead of nesting it under BasePath.
+	return u.JoinPath(atmosConfig.BasePath, atmosConfig.Vendor.BasePath)
+}
+
 // Helper function to resolve the vendor config file path.
 func resolveVendorConfigFilePath(atmosConfig *schema.AtmosConfiguration, vendorConfigFile string, checkGlobalConfig bool) string {
 	if checkGlobalConfig && atmosConfig.Vendor.BasePath != "" {
 		if !filepath.IsAbs(atmosConfig.Vendor.BasePath) {
-			return filepath.Join(atmosConfig.BasePath, atmosConfig.Vendor.BasePath)
+			return getVendorDirToUse(atmosConfig)
 		}
 		return atmosConfig.Vendor.BasePath
 	}
 
 	// Search for the vendor config file
 	foundVendorConfigFile, fileExists := u.SearchConfigFile(vendorConfigFile)
 	if !fileExists {
-		pathToVendorConfig := filepath.Join(atmosConfig.BasePath, vendorConfigFile)
+		pathToVendorConfig := filepath.Join(getBasePathToUse(atmosConfig), vendorConfigFile)
 		foundVendorConfigFile, fileExists = u.SearchConfigFile(pathToVendorConfig)
 		if !fileExists {
 			return "" // File does not exist, but this is not an error
@@ -228,7 +243,9 @@ func ExecuteAtmosVendorInternal(params *executeVendorOptions) error {
 	var err error
 	vendorConfigFilePath := filepath.Dir(params.vendorConfigFileName)
 
-	logInitialMessage(params.vendorConfigFileName, params.tags)
+	// displayPath keeps the log message short and machine-independent; params.vendorConfigFileName
+	// itself stays untouched (and possibly absolute) for the actual file/source resolution below.
+	logInitialMessage(displayPath(params.vendorConfigFileName), params.tags)
 	if len(params.atmosVendorSpec.Sources) == 0 && len(params.atmosVendorSpec.Imports) == 0 {
 		return fmt.Errorf("%w '%s'", ErrMissingVendorConfigDefinition, params.vendorConfigFileName)
 	}

internal/exec/workflow.go

@@ -142,7 +142,7 @@ func ExecuteWorkflowCmd(cmd *cobra.Command, args []string) error {
 	if u.IsPathAbsolute(workflowFile) {
 		workflowPath = workflowFile
 	} else {
-		workflowPath = filepath.Join(atmosConfig.BasePath, atmosConfig.Workflows.BasePath, workflowFile)
+		workflowPath = filepath.Join(getWorkflowsDirToUse(&atmosConfig), workflowFile)
 	}
 
 	// If the workflow file is specified without an extension, use the default extension
@@ -154,7 +154,7 @@ func ExecuteWorkflowCmd(cmd *cobra.Command, args []string) error {
 
 	if !u.FileExists(workflowPath) {
 		return errUtils.Build(errUtils.ErrWorkflowFileNotFound).
-			WithExplanationf("The workflow manifest file `%s` does not exist", filepath.ToSlash(workflowPath)).
+			WithExplanationf("The workflow manifest file `%s` does not exist", filepath.ToSlash(displayPath(workflowPath))).
 			WithExitCode(1).
 			Err()
 	}
@@ -175,7 +175,7 @@ func ExecuteWorkflowCmd(cmd *cobra.Command, args []string) error {
 
 	if workflowManifest.Workflows == nil {
 		return errUtils.Build(errUtils.ErrInvalidWorkflowManifest).
-			WithExplanationf("The workflow manifest `%s` must be a map with the top-level `workflows:` key", filepath.ToSlash(workflowPath)).
+			WithExplanationf("The workflow manifest `%s` must be a map with the top-level `workflows:` key", filepath.ToSlash(displayPath(workflowPath))).
 			WithHint("Add a top-level 'workflows:' key to the manifest file").
 			WithExitCode(1).
 			Err()

internal/exec/workflow_utils.go

@@ -944,8 +944,14 @@ func ExecuteWorkflow(
 			stepErr := err
 			if !errors.Is(err, errUtils.ErrInvalidWorkflowStepType) {
 				stepErr = buildWorkflowStepError(err, &workflowStepErrorContext{
-					WorkflowPath:     workflowPath,
-					WorkflowBasePath: atmosConfig.Workflows.BasePath,
+					WorkflowPath: workflowPath,
+					// Must be the SAME anchor workflowPath was actually joined against
+					// (workflow.go), not the raw, always-relative atmosConfig.Workflows.BasePath
+					// -- otherwise the TrimPrefix below in buildWorkflowStepError silently fails
+					// to strip it whenever workflowPath ends up absolute (e.g. via the
+					// precomputed WorkflowsDirAbsolutePath), leaving the resume-command hint
+					// showing a garbled path instead of the plain workflow file name.
+					WorkflowBasePath: getWorkflowsDirToUse(&atmosConfig),
 					Workflow:         workflow,
 					StepName:         step.Name,
 					Command:          command,
@@ -1098,12 +1104,15 @@ func ExecuteDescribeWorkflows(
 		return nil, nil, nil, errUtils.ErrWorkflowBasePathNotConfigured
 	}
 
-	// If `workflows.base_path` is a relative path, join it with `stacks.base_path`
+	// If `workflows.base_path` is a relative path, resolve it via getWorkflowsDirToUse
+	// (prefers the precomputed WorkflowsDirAbsolutePath over the raw, possibly still-relative
+	// atmosConfig.BasePath -- same bug shape cloudposse/atmos#2864 fixed for the top-level
+	// base_path itself).
 	var workflowsDir string
 	if u.IsPathAbsolute(atmosConfig.Workflows.BasePath) {
 		workflowsDir = atmosConfig.Workflows.BasePath
 	} else {
-		workflowsDir = filepath.Join(atmosConfig.BasePath, atmosConfig.Workflows.BasePath)
+		workflowsDir = getWorkflowsDirToUse(&atmosConfig)
 	}
 
 	isDirectory, err := u.IsDirectory(workflowsDir)
@@ -1122,7 +1131,7 @@ func ExecuteDescribeWorkflows(
 		if u.IsPathAbsolute(atmosConfig.Workflows.BasePath) {
 			workflowPath = filepath.Join(atmosConfig.Workflows.BasePath, f)
 		} else {
-			workflowPath = filepath.Join(atmosConfig.BasePath, atmosConfig.Workflows.BasePath, f)
+			workflowPath = filepath.Join(getWorkflowsDirToUse(&atmosConfig), f)
 		}
 
 		fileContent, err := os.ReadFile(workflowPath)

pkg/config/base_path_resolution_test.go

@@ -739,8 +739,17 @@ func TestInitCliConfig_BasePathSource_SetForEnvVar(t *testing.T) {
 		"BasePathSource should be 'runtime' when ATMOS_BASE_PATH env var is set")
 }
 
-// TestFindAllStackConfigsInPathsForStack_ErrorWrapping verifies that when GetGlobMatches
-// fails, the error is wrapped with the ErrFailedToFindImport sentinel.
+// TestFindAllStackConfigsInPathsForStack_ErrorWrapping verifies that when every
+// included_paths entry matches nothing (e.g. the whole stacks directory doesn't exist),
+// the function still errors -- with ErrNoStackManifestsFound, not ErrFailedToFindImport.
+//
+// Prior to cloudposse/atmos#2867's fix, a single entry matching nothing surfaced
+// ErrFailedToFindImport directly from inside the per-path loop, which also meant a SECOND,
+// valid included_paths entry earlier in the list would have its already-found matches
+// discarded by this same hard error. Now, an individual entry matching nothing is treated as
+// "nothing here, keep looking" and only the aggregate "nothing matched at all" case (this
+// test: the only entry present matches nothing) errors, with a sentinel describing that
+// outcome directly instead of leaking the glob-matching implementation's own error identity.
 func TestFindAllStackConfigsInPathsForStack_ErrorWrapping(t *testing.T) {
 	atmosConfig := schema.AtmosConfiguration{
 		StacksBaseAbsolutePath: filepath.Join(os.TempDir(), "nonexistent-stacks-dir-test"),
@@ -759,11 +768,13 @@ func TestFindAllStackConfigsInPathsForStack_ErrorWrapping(t *testing.T) {
 
 	require.Error(t, err)
 
-	assert.True(t, errors.Is(err, errUtils.ErrFailedToFindImport),
-		"Error should wrap ErrFailedToFindImport, got: %v", err)
+	assert.True(t, errors.Is(err, errUtils.ErrNoStackManifestsFound),
+		"Error should wrap ErrNoStackManifestsFound, got: %v", err)
 }
 
-// TestFindAllStackConfigsInPaths_ErrorWrapping verifies error wrapping in the non-stack variant.
+// TestFindAllStackConfigsInPaths_ErrorWrapping verifies error wrapping in the non-stack
+// variant. See TestFindAllStackConfigsInPathsForStack_ErrorWrapping above for why this is
+// ErrNoStackManifestsFound rather than ErrFailedToFindImport post-#2867.
 func TestFindAllStackConfigsInPaths_ErrorWrapping(t *testing.T) {
 	atmosConfig := schema.AtmosConfiguration{
 		StacksBaseAbsolutePath: filepath.Join(os.TempDir(), "nonexistent-stacks-dir-test2"),
@@ -781,6 +792,6 @@ func TestFindAllStackConfigsInPaths_ErrorWrapping(t *testing.T) {
 
 	require.Error(t, err)
 
-	assert.True(t, errors.Is(err, errUtils.ErrFailedToFindImport),
-		"Error should wrap ErrFailedToFindImport, got: %v", err)
+	assert.True(t, errors.Is(err, errUtils.ErrNoStackManifestsFound),
+		"Error should wrap ErrNoStackManifestsFound, got: %v", err)
 }

pkg/config/config.go

@@ -524,6 +524,25 @@ func AtmosConfigAbsolutePaths(atmosConfig *schema.AtmosConfiguration) error {
 	}
 	atmosConfig.HelmDirAbsolutePath = helmDirAbsPath
 
+	// Convert Vendor base path to an absolute path. Consumers previously re-joined the raw
+	// (possibly still-relative) atmosConfig.BasePath at call time instead of using a
+	// precomputed absolute path -- the same bug shape #2864 fixed for the top-level
+	// base_path itself, just not yet applied here.
+	vendorBasePath := u.JoinPath(atmosBasePathAbs, atmosConfig.Vendor.BasePath)
+	vendorDirAbsPath, err := absPathOrError(vendorBasePath, "vendor base path")
+	if err != nil {
+		return err
+	}
+	atmosConfig.VendorDirAbsolutePath = vendorDirAbsPath
+
+	// Convert Workflows base path to an absolute path (same rationale as Vendor above).
+	workflowsBasePath := u.JoinPath(atmosBasePathAbs, atmosConfig.Workflows.BasePath)
+	workflowsDirAbsPath, err := absPathOrError(workflowsBasePath, "workflows base path")
+	if err != nil {
+		return err
+	}
+	atmosConfig.WorkflowsDirAbsolutePath = workflowsDirAbsPath
+
 	return nil
 }