fix: disable pager mouse interactions and add global --pager flag (#1430)

* fix: disable pager mouse interactions and add global --pager flag

- Remove tea.WithMouseCellMotion() to enable mouse text selection in pager
- Change pager default from enabled to disabled for better scripting/automation
- Add global --pager flag supporting true/false/command values
- Add color field to terminal settings (deprecates no_color in config)
- Support ATMOS_COLOR and COLOR environment variables
- Update documentation with new global-flags.mdx page
- Add comprehensive tests for pager and color functionality

BREAKING CHANGE: Pager is now disabled by default. Use --pager flag or set pager: true in atmos.yaml to enable.

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Co-Authored-By: Claude <noreply@anthropic.com>

* [autofix.ci] apply automated fixes

* fix: address PR feedback - improve code quality and documentation accuracy

- Replace if-else chain with switch statement for better readability (cmd/root.go)
- Fix documentation: move Stack/Component flags to Command-Specific section
- Remove Breaking Change section from documentation (better suited for release notes)

These changes address code quality concerns raised by GitHub's advanced security
scanner and improve the accuracy of the documentation.

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Co-Authored-By: Claude <noreply@anthropic.com>

* fix: address PR feedback - improve code quality and robustness

This commit addresses comprehensive feedback from PR review covering
code quality, documentation accuracy, test coverage, and consistency.

Changes implemented:
• Fix case/whitespace handling in pager value parsing (schema.go)
• Enhance --pager documentation with examples and quoting guidance
• Fix --no-color flag parsing to properly handle true/false values
• Remove redundant per-command pager logic in favor of global handling
• Replace direct NoColor field access with IsColorEnabled() method
• Fix log level comparison to use canonical constants instead of strings
• Add comprehensive test coverage for PAGER env vars and flag precedence

Technical improvements:
- Pager values now normalized with strings.ToLower(strings.TrimSpace())
- Flag parsing avoids variable shadowing and properly validates values
- Removed conflicting per-command pager overrides
- Enhanced environment variable precedence testing
- Documentation includes practical examples for shell quoting

All existing tests pass with improved coverage and robustness.

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Co-Authored-By: Claude <noreply@anthropic.com>

* fix: change default log level from Info to Warning and update tests

This change reduces Atmos output verbosity by changing the default log
level from Info to Warning. Also fixes global flags documentation by
removing non-global flag sections.

- Change default log level from "Info" to "Warning" in config files
- Update all test files to use "Warning" instead of "Info" as default
- Remove non-global flag sections from global-flags.mdx documentation
- Update documentation examples to reflect new default log level

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Co-Authored-By: Claude <noreply@anthropic.com>

* fix: final packer test cleanup and documentation refinements

- Fix logger level inconsistencies in packer tests (use WarnLevel to match ATMOS_LOGS_LEVEL=Warning)
- Add proper resource cleanup with defer blocks to prevent writes to closed pipes
- Remove misleading PAGER=cat reference from CI/CD example in global-flags.mdx
- Replace with proper ATMOS_PAGER=off for pager disabling
- Fix backslash escaping issues in test assertions

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Co-Authored-By: Claude <noreply@anthropic.com>

* fix: add missing viper import in config_test.go

- Add viper import required for TestEnvironmentVariableHandling test function
- Resolves undefined viper error after merge conflict resolution

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Co-Authored-By: Claude <noreply@anthropic.com>

* feat: add NO_PAGER environment variable support and improve documentation

- Add NO_PAGER environment variable support following standard CLI conventions
- Implement proper precedence: CLI flags > NO_PAGER > ATMOS_PAGER > PAGER > config
- Add comprehensive test coverage for NO_PAGER functionality (6 new test cases)
- Update global-flags.mdx with NO_PAGER documentation and examples
- Improve terminal.mdx by removing redundant deprecation warnings
- Add clear configuration precedence documentation for pager and color settings
- Focus on promoting current best practices rather than deprecated features

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Co-Authored-By: Claude <noreply@anthropic.com>

* [autofix.ci] apply automated fixes

* fix: enable pager in TestDescribeAffected mock expectations

- Initialize atmosConfig with proper Terminal.Pager settings
- Set Pager to "false" initially when pager should be disabled
- Enable Pager to "true" for tests expecting pager.Run() calls
- Ensures mock expectations align with actual pager invocation logic
- Fix linting issue: use tagged switch instead of if-else

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Co-Authored-By: Claude <noreply@anthropic.com>

* fix: correct pager flag syntax in TestExecuteDescribeComponentCmd_Success_YAMLWithPager

- Change `--pager more` to `--pager=more` to fix flag parsing issue
- Cobra was treating `more` as a separate argument instead of the pager value
- This was causing "Unknown command component-1" errors in tests

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Co-Authored-By: Claude <noreply@anthropic.com>

* fix: resolve contradictory color configuration and update snapshots

- Set default value for settings.terminal.color to true in config
- Ensures consistent color configuration: color=true, no_color=false by default
- Color is enabled by default when TTY is detected, as intended
- Update golden snapshots for config output to include color: true
- Update help snapshots to include new global --pager flag
- Fixes contradictory config where both color=false and no_color=false appeared
- Fix linting issues: add period to comment and alias log import

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Co-Authored-By: Claude <noreply@anthropic.com>

* fix: improve documentation and test cleanup for pager and logger

- Add GoDoc comment to IsPagerEnabled method describing its purpose and return value
- Fix inline comments to be complete sentences with proper punctuation
- Fix packer validate and version tests to properly handle logger levels:
  - Set logger level to Warning to match ATMOS_LOGS_LEVEL environment variable
  - Restore original logger level and output using defer for proper cleanup
  - Prevent writing to closed pipes by restoring logger output to os.Stderr

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Co-Authored-By: Claude <noreply@anthropic.com>

* fix: increase Windows retry delays for better CI reliability

- Increase initial retry delay from 100ms to 200ms
- Increase progressive delays to 200ms, 500ms, 1000ms
- Increase file operation delay to 200ms
- These changes improve reliability of Windows GitHub Actions runners
  by giving file operations more time to complete

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* fix: update Windows delay test expectations to match increased retry delays

- Update TestWindowsFileDelay to expect 200ms delay (was 150ms max)
- Update retry test timing expectations for new delay values
- TestRetryOnWindows_RetryThenSuccess: expect 650ms+ (was 250ms+)
- TestRetryOnWindows_AllFailures: expect 650ms+ (was 250ms+)
- Comments updated to reflect actual delay values: 200ms, 500ms, 1000ms

This fixes the TestWindowsFileDelay test failure caused by increasing
windowsFileDelay from 100ms to 200ms to improve Windows CI reliability.

The original terraform_output_function_(no_tty) test is now passing.

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Co-Authored-By: Claude <noreply@anthropic.com>

* fix: improve log level comparison and reduce complexity in validate_editorconfig

- Replace direct string comparison with logger.ParseLogLevel() for consistent
  log level parsing in cmd/validate_editorconfig.go
- Refactor nested if statements to reduce complexity (nestif linter)
- Extract boolean variables to clarify logic for trace level detection
- Added import for github.com/cloudposse/atmos/pkg/logger package

The PAGER=cat documentation requested for update was not found in the current
website/docs/cli/global-flags.mdx file at the specified location.

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Co-Authored-By: Claude <noreply@anthropic.com>

* docs: clarify pager settings and improve terminal documentation structure

- Fix confusing categorization of pager settings in terminal.mdx
- Clarify that there are TWO different pager settings:
  1. Terminal.Pager: Main pager for all terminal output
  2. SyntaxHighlighting.Pager: Separate pager for syntax-highlighted content
- Update YAML example to show both settings and their different purposes
- Improve description of syntax highlighting pager to clarify it's separate
  from the main terminal pager setting
- Add comments in YAML example to distinguish terminal vs syntax settings

This resolves confusion where pager appeared to be incorrectly categorized
as a syntax highlighting setting when it's actually a terminal setting.

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Co-Authored-By: Claude <noreply@anthropic.com>

* refactor: remove unused syntax_highlighting.pager setting

- Remove HighlightedOutputPager field from SyntaxHighlighting struct
- Remove unused pager setting from highlight defaults and configurations
- Update tests to remove references to unused syntax highlighting pager
- Clean up documentation to remove confusing syntax highlighting pager
- Simplify YAML example to only show implemented terminal settings

The syntax_highlighting.pager setting was defined in the schema and set
in defaults, but never actually used anywhere in the codebase. It was
dead code that created confusion about pager functionality.

Only the main Terminal.Pager setting is functional and controls all
terminal output paging behavior.

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Co-Authored-By: Claude <noreply@anthropic.com>

* docs: improve NO_PAGER comment to explain negative boolean logic

Expand the nolint comment to clearly explain why NO_PAGER uses direct
os.Getenv() instead of viper.BindEnv():

1. NO_PAGER uses negative logic (NO_PAGER=true disables pager)
2. Atmos config uses positive boolean names (pager: true enables pager)
3. We don't want a confusing "no_pager" config field in the schema
4. NO_PAGER should remain environment-only, not a config file setting

This clarifies the design decision to keep NO_PAGER as a standard CLI
environment variable convention rather than making it configurable.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* test: update snapshots to remove syntax_highlighting.pager references

Regenerate golden snapshots for:
- TestCLICommands_atmos_describe_config_imports.stdout.golden
- TestCLICommands_atmos_describe_configuration.stdout.golden

These snapshots were expecting `pager: false` under the `syntax_highlighting`
section, but this field was removed as unused dead code.

The snapshots now correctly reflect the current schema structure without
the unused HighlightedOutputPager field.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* test: update remaining snapshots to remove syntax_highlighting.pager references

Updates three test snapshots that still contained references to the removed
syntax_highlighting.pager setting:
- TestCLICommands_indentation.stdout.golden
- TestCLICommands_atmos_describe_config_-f_yaml.stdout.golden
- TestCLICommands_atmos_describe_config.stdout.golden

This completes the cleanup from the previous refactoring that removed the
unused syntax_highlighting.pager configuration option.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* fix: remove remaining pager reference from test fixture

Removes the last remaining `pager: false` reference from the test fixture
at tests/fixtures/scenarios/atmos-describe-affected-with-dependents-and-locked/atmos.yaml.

This completes the cleanup of all syntax_highlighting.pager references that
were causing Windows acceptance test failures due to snapshot mismatches.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

---------

Co-authored-by: Claude <noreply@anthropic.com>
Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com>
Co-authored-by: Andriy Knysh <aknysh@users.noreply.github.com>

Author: 4 people

atmos.yaml

@@ -352,7 +352,7 @@ settings:
   # Terminal settings for displaying content
   terminal:
     max_width: 120          # Maximum width for terminal output
-    pager: true             # Pager setting for all terminal output
+    pager: false            # Pager setting for all terminal output
     unicode: true           # Use unicode characters
 
     syntax_highlighting:

cmd/describe.go

@@ -15,7 +15,6 @@ var describeCmd = &cobra.Command{
 
 func init() {
 	describeCmd.PersistentFlags().StringP("query", "q", "", "Query the results of an `atmos describe` command using `yq` expressions")
-	describeCmd.PersistentFlags().String("pager", "true", "Disable / Enable the paging user experience")
 
 	RootCmd.AddCommand(describeCmd)
 }

cmd/describe_affected.go

@@ -70,13 +70,7 @@ func getRunnableDescribeAffectedCmd(
 			}
 		}
 
-		if cmd.Flags().Changed("pager") {
-			// TODO: update this post pr:https://github.com/cloudposse/atmos/pull/1174 is merged
-			props.CLIConfig.Settings.Terminal.Pager, err = cmd.Flags().GetString("pager")
-			if err != nil {
-				return err
-			}
-		}
+		// Global --pager flag is now handled in cfg.InitCliConfig
 
 		err = newDescribeAffectedExec(props.CLIConfig).Execute(&props)
 		return err

cmd/describe_component.go

@@ -61,11 +61,6 @@ var describeComponentCmd = &cobra.Command{
 			return err
 		}
 
-		pager, err := flags.GetString("pager")
-		if err != nil {
-			return err
-		}
-
 		component := args[0]
 
 		err = e.NewDescribeComponentExec().ExecuteDescribeComponentCmd(e.DescribeComponentParams{
@@ -75,7 +70,6 @@ var describeComponentCmd = &cobra.Command{
 			ProcessYamlFunctions: processYamlFunctions,
 			Skip:                 skip,
 			Query:                query,
-			Pager:                pager,
 			Format:               format,
 			File:                 file,
 		})

cmd/describe_config.go

@@ -33,13 +33,7 @@ var describeConfigCmd = &cobra.Command{
 			return err
 		}
 
-		if cmd.Flags().Changed("pager") {
-			// TODO: update this post pr:https://github.com/cloudposse/atmos/pull/1174 is merged
-			atmosConfig.Settings.Terminal.Pager, err = cmd.Flags().GetString("pager")
-			if err != nil {
-				return err
-			}
-		}
+		// Global --pager flag is now handled in cfg.InitCliConfig
 
 		err = e.NewDescribeConfig(&atmosConfig).ExecuteDescribeConfigCmd(query, format, "")
 		return err

cmd/describe_dependents.go

@@ -54,12 +54,7 @@ func getRunnableDescribeDependentsCmd(
 			return err
 		}
 
-		if cmd.Flags().Changed("pager") {
-			atmosConfig.Settings.Terminal.Pager, err = cmd.Flags().GetString("pager")
-			if err != nil {
-				return err
-			}
-		}
+		// Global --pager flag is now handled in cfg.InitCliConfig
 
 		describe.Component = args[0]
 		err = newDescribeDependentsExec(&atmosConfig).Execute(describe)

cmd/describe_stacks.go

@@ -70,13 +70,7 @@ func getRunnableDescribeStacksCmd(
 			return err
 		}
 
-		if cmd.Flags().Changed("pager") {
-			// TODO: update this post pr:https://github.com/cloudposse/atmos/pull/1174 is merged
-			atmosConfig.Settings.Terminal.Pager, err = cmd.Flags().GetString("pager")
-			if err != nil {
-				return err
-			}
-		}
+		// Global --pager flag is now handled in cfg.InitCliConfig
 
 		err = g.newDescribeStacksExec.Execute(&atmosConfig, describe)
 		return err

cmd/describe_workflows.go

@@ -52,12 +52,7 @@ func getRunnableDescribeWorkflowsCmd(
 			return err
 		}
 
-		pager, err := cmd.Flags().GetString("pager")
-		if err != nil {
-			return err
-		}
-
-		atmosConfig.Settings.Terminal.Pager = pager
+		// Global --pager flag is now handled in cfg.InitCliConfig
 		err = describeWorkflowsExec.Execute(&atmosConfig, describeWorkflowArgs)
 		return err
 	}

cmd/packer_init_test.go

@@ -11,8 +11,8 @@ func TestPackerInitCmd(t *testing.T) {
 	workDir := "../tests/fixtures/scenarios/packer"
 	t.Setenv("ATMOS_CLI_CONFIG_PATH", workDir)
 	t.Setenv("ATMOS_BASE_PATH", workDir)
-	t.Setenv("ATMOS_LOGS_LEVEL", "Info")
-	log.SetLevel(log.InfoLevel)
+	t.Setenv("ATMOS_LOGS_LEVEL", "Warning")
+	log.SetLevel(log.WarnLevel)
 
 	RootCmd.SetArgs([]string{"packer", "init", "aws/bastion", "-s", "nonprod"})
 	err := Execute()

cmd/packer_inspect_test.go

@@ -14,22 +14,27 @@ func TestPackerInspectCmd(t *testing.T) {
 	workDir := "../tests/fixtures/scenarios/packer"
 	t.Setenv("ATMOS_CLI_CONFIG_PATH", workDir)
 	t.Setenv("ATMOS_BASE_PATH", workDir)
-	t.Setenv("ATMOS_LOGS_LEVEL", "Info")
-	log.SetLevel(log.InfoLevel)
+	t.Setenv("ATMOS_LOGS_LEVEL", "Warning")
+	log.SetLevel(log.WarnLevel)
 
 	oldStd := os.Stdout
 	r, w, _ := os.Pipe()
 	os.Stdout = w
 	log.SetOutput(w)
 
+	// Ensure cleanup happens before any reads
+	defer func() {
+		os.Stdout = oldStd
+		log.SetOutput(os.Stderr)
+	}()
+
 	RootCmd.SetArgs([]string{"packer", "inspect", "aws/bastion", "-s", "nonprod"})
 	err := Execute()
 	assert.NoError(t, err, "'TestPackerInspectCmd' should execute without error")
 
-	// Restore std
+	// Close write end after Execute
 	err = w.Close()
 	assert.NoError(t, err)
-	os.Stdout = oldStd
 
 	// Read the captured output
 	var buf bytes.Buffer