Migrate pkg/repos to Medium abstraction (#291)

* chore(io): Migrate pkg/repos to Medium abstraction

- Modified Registry and Repo structs in pkg/repos/registry.go to include io.Medium.
- Updated LoadRegistry, FindRegistry, and ScanDirectory signatures to accept io.Medium.
- Migrated all internal file operations in pkg/repos/registry.go to use the Medium interface instead of io.Local or os package.
- Updated dozens of call sites across internal/cmd/ to pass io.Local to the updated repos functions.
- Ensured consistent use of io.Medium for repo existence and git checks.

* chore(io): Fix undefined io errors in repos migration

- Fixed "undefined: io" compilation errors by using the correct 'coreio' alias in internal commands.
- Corrected FindRegistry and LoadRegistry calls in cmd_file_sync.go, cmd_install.go, and cmd_search.go.
- Verified fix with successful project-wide build.

* chore(io): Final fixes for repos Medium migration

- Fixed formatting issue in internal/cmd/setup/cmd_github.go by using 'coreio' alias for consistency.
- Ensured all callers use the 'coreio' alias when referring to the io package.
- Verified project-wide build completes successfully.

* chore(io): Complete migration of pkg/repos to io.Medium

- Migrated pkg/repos/registry.go to use io.Medium abstraction for all file operations.
- Updated all callers in internal/cmd/ to pass io.Local, with proper alias handling.
- Fixed formatting issues in cmd_github.go that caused previous CI failures.
- Added unit tests in pkg/repos/registry_test.go using io.MockMedium.
- Verified project-wide build and new unit tests pass.

* chore(io): Address PR feedback for Medium migration

- Made pkg/repos truly medium-agnostic by removing local filepath.Abs calls.
- Restored Medium abstraction in pkg/cli/daemon.go (PIDFile and Daemon).
- Restored context cancellation checks in pkg/container/linuxkit.go.
- Updated pkg/cli/daemon_test.go to use MockMedium.
- Documented FindRegistry's local filesystem dependencies.
- Verified project-wide build and tests pass.

* chore(io): Fix merge conflicts and address PR feedback

- Resolved merge conflicts with latest dev branch.
- Restored Medium abstraction in pkg/cli/daemon.go and context checks in pkg/container/linuxkit.go.
- Refactored pkg/repos/registry.go to be truly medium-agnostic (removed filepath.Abs).
- Updated pkg/cli/daemon_test.go to use MockMedium.
- Verified all builds and tests pass locally.

* chore(io): Complete pkg/repos Medium migration and PR feedback

- Refactored pkg/repos to use io.Medium abstraction, removing local filesystem dependencies.
- Updated all call sites in internal/cmd to pass io.Local/coreio.Local.
- Restored Medium abstraction in pkg/cli/daemon.go and context checks in pkg/container/linuxkit.go.
- Updated pkg/cli/daemon_test.go to use MockMedium for better test isolation.
- Fixed merge conflicts and code formatting issues.
- Verified project-wide build and tests pass.

* fix(lint): handle error return values in registry tests

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

internal/cmd/dev/cmd_apply.go

@@ -225,12 +225,12 @@ func runApply() error {
 // getApplyTargetRepos gets repos to apply command to
 func getApplyTargetRepos() ([]*repos.Repo, error) {
 	// Load registry
-	registryPath, err := repos.FindRegistry()
+	registryPath, err := repos.FindRegistry(io.Local)
 	if err != nil {
 		return nil, core.E("dev.apply", "failed to find registry", err)
 	}
 
-	registry, err := repos.LoadRegistry(registryPath)
+	registry, err := repos.LoadRegistry(io.Local, registryPath)
 	if err != nil {
 		return nil, core.E("dev.apply", "failed to load registry", err)
 	}

internal/cmd/dev/cmd_ci.go

@@ -10,6 +10,7 @@ import (
 
 	"github.com/host-uk/core/pkg/cli"
 	"github.com/host-uk/core/pkg/i18n"
+	"github.com/host-uk/core/pkg/io"
 	"github.com/host-uk/core/pkg/repos"
 )
 
@@ -75,20 +76,20 @@ func runCI(registryPath string, branch string, failedOnly bool) error {
 	var err error
 
 	if registryPath != "" {
-		reg, err = repos.LoadRegistry(registryPath)
+		reg, err = repos.LoadRegistry(io.Local, registryPath)
 		if err != nil {
 			return cli.Wrap(err, "failed to load registry")
 		}
 	} else {
-		registryPath, err = repos.FindRegistry()
+		registryPath, err = repos.FindRegistry(io.Local)
 		if err == nil {
-			reg, err = repos.LoadRegistry(registryPath)
+			reg, err = repos.LoadRegistry(io.Local, registryPath)
 			if err != nil {
 				return cli.Wrap(err, "failed to load registry")
 			}
 		} else {
 			cwd, _ := os.Getwd()
-			reg, err = repos.ScanDirectory(cwd)
+			reg, err = repos.ScanDirectory(io.Local, cwd)
 			if err != nil {
 				return cli.Wrap(err, "failed to scan directory")
 			}

internal/cmd/dev/cmd_file_sync.go

@@ -195,12 +195,12 @@ func runFileSync(source string) error {
 // resolveTargetRepos resolves the --to pattern to actual repos
 func resolveTargetRepos(pattern string) ([]*repos.Repo, error) {
 	// Load registry
-	registryPath, err := repos.FindRegistry()
+	registryPath, err := repos.FindRegistry(coreio.Local)
 	if err != nil {
 		return nil, log.E("dev.sync", "failed to find registry", err)
 	}
 
-	registry, err := repos.LoadRegistry(registryPath)
+	registry, err := repos.LoadRegistry(coreio.Local, registryPath)
 	if err != nil {
 		return nil, log.E("dev.sync", "failed to load registry", err)
 	}

internal/cmd/dev/cmd_impact.go

@@ -6,6 +6,7 @@ import (
 
 	"github.com/host-uk/core/pkg/cli"
 	"github.com/host-uk/core/pkg/i18n"
+	"github.com/host-uk/core/pkg/io"
 	"github.com/host-uk/core/pkg/repos"
 )
 
@@ -42,14 +43,14 @@ func runImpact(registryPath string, repoName string) error {
 	var err error
 
 	if registryPath != "" {
-		reg, err = repos.LoadRegistry(registryPath)
+		reg, err = repos.LoadRegistry(io.Local, registryPath)
 		if err != nil {
 			return cli.Wrap(err, "failed to load registry")
 		}
 	} else {
-		registryPath, err = repos.FindRegistry()
+		registryPath, err = repos.FindRegistry(io.Local)
 		if err == nil {
-			reg, err = repos.LoadRegistry(registryPath)
+			reg, err = repos.LoadRegistry(io.Local, registryPath)
 			if err != nil {
 				return cli.Wrap(err, "failed to load registry")
 			}

internal/cmd/dev/registry.go

@@ -8,6 +8,7 @@ import (
 	"github.com/host-uk/core/internal/cmd/workspace"
 	"github.com/host-uk/core/pkg/cli"
 	"github.com/host-uk/core/pkg/i18n"
+	"github.com/host-uk/core/pkg/io"
 	"github.com/host-uk/core/pkg/repos"
 )
 
@@ -18,16 +19,16 @@ func loadRegistryWithConfig(registryPath string) (*repos.Registry, string, error
 	var registryDir string
 
 	if registryPath != "" {
-		reg, err = repos.LoadRegistry(registryPath)
+		reg, err = repos.LoadRegistry(io.Local, registryPath)
 		if err != nil {
 			return nil, "", cli.Wrap(err, "failed to load registry")
 		}
 		cli.Print("%s %s\n\n", dimStyle.Render(i18n.Label("registry")), registryPath)
 		registryDir = filepath.Dir(registryPath)
 	} else {
-		registryPath, err = repos.FindRegistry()
+		registryPath, err = repos.FindRegistry(io.Local)
 		if err == nil {
-			reg, err = repos.LoadRegistry(registryPath)
+			reg, err = repos.LoadRegistry(io.Local, registryPath)
 			if err != nil {
 				return nil, "", cli.Wrap(err, "failed to load registry")
 			}
@@ -36,7 +37,7 @@ func loadRegistryWithConfig(registryPath string) (*repos.Registry, string, error
 		} else {
 			// Fallback: scan current directory
 			cwd, _ := os.Getwd()
-			reg, err = repos.ScanDirectory(cwd)
+			reg, err = repos.ScanDirectory(io.Local, cwd)
 			if err != nil {
 				return nil, "", cli.Wrap(err, "failed to scan directory")
 			}

internal/cmd/docs/cmd_scan.go

@@ -30,22 +30,22 @@ func loadRegistry(registryPath string) (*repos.Registry, string, error) {
 	var registryDir string
 
 	if registryPath != "" {
-		reg, err = repos.LoadRegistry(registryPath)
+		reg, err = repos.LoadRegistry(io.Local, registryPath)
 		if err != nil {
 			return nil, "", cli.Wrap(err, i18n.T("i18n.fail.load", "registry"))
 		}
 		registryDir = filepath.Dir(registryPath)
 	} else {
-		registryPath, err = repos.FindRegistry()
+		registryPath, err = repos.FindRegistry(io.Local)
 		if err == nil {
-			reg, err = repos.LoadRegistry(registryPath)
+			reg, err = repos.LoadRegistry(io.Local, registryPath)
 			if err != nil {
 				return nil, "", cli.Wrap(err, i18n.T("i18n.fail.load", "registry"))
 			}
 			registryDir = filepath.Dir(registryPath)
 		} else {
 			cwd, _ := os.Getwd()
-			reg, err = repos.ScanDirectory(cwd)
+			reg, err = repos.ScanDirectory(io.Local, cwd)
 			if err != nil {
 				return nil, "", cli.Wrap(err, i18n.T("i18n.fail.scan", "directory"))
 			}

internal/cmd/doctor/cmd_environment.go

@@ -8,6 +8,7 @@ import (
 	"strings"
 
 	"github.com/host-uk/core/pkg/i18n"
+	"github.com/host-uk/core/pkg/io"
 	"github.com/host-uk/core/pkg/repos"
 )
 
@@ -43,11 +44,11 @@ func checkGitHubCLI() bool {
 
 // checkWorkspace checks for repos.yaml and counts cloned repos
 func checkWorkspace() {
-	registryPath, err := repos.FindRegistry()
+	registryPath, err := repos.FindRegistry(io.Local)
 	if err == nil {
 		fmt.Printf("  %s %s\n", successStyle.Render("✓"), i18n.T("cmd.doctor.repos_yaml_found", map[string]interface{}{"Path": registryPath}))
 
-		reg, err := repos.LoadRegistry(registryPath)
+		reg, err := repos.LoadRegistry(io.Local, registryPath)
 		if err == nil {
 			basePath := reg.BasePath
 			if basePath == "" {

internal/cmd/monitor/cmd_monitor.go

@@ -18,6 +18,7 @@ import (
 
 	"github.com/host-uk/core/pkg/cli"
 	"github.com/host-uk/core/pkg/i18n"
+	"github.com/host-uk/core/pkg/io"
 	"github.com/host-uk/core/pkg/log"
 	"github.com/host-uk/core/pkg/repos"
 )
@@ -177,12 +178,12 @@ func resolveRepos() ([]string, error) {
 
 	if monitorAll {
 		// All repos from registry
-		registry, err := repos.FindRegistry()
+		registry, err := repos.FindRegistry(io.Local)
 		if err != nil {
 			return nil, log.E("monitor", "failed to find registry", err)
 		}
 
-		loaded, err := repos.LoadRegistry(registry)
+		loaded, err := repos.LoadRegistry(io.Local, registry)
 		if err != nil {
 			return nil, log.E("monitor", "failed to load registry", err)
 		}

internal/cmd/pkgcmd/cmd_install.go

@@ -51,8 +51,8 @@ func runPkgInstall(repoArg, targetDir string, addToRegistry bool) error {
 
 	// Determine target directory
 	if targetDir == "" {
-		if regPath, err := repos.FindRegistry(); err == nil {
+		if regPath, err := repos.FindRegistry(coreio.Local); err == nil {
-			if reg, err := repos.LoadRegistry(regPath); err == nil {
+			if reg, err := repos.LoadRegistry(coreio.Local, regPath); err == nil {
 				targetDir = reg.BasePath
 				if targetDir == "" {
 					targetDir = "./packages"
@@ -110,12 +110,12 @@ func runPkgInstall(repoArg, targetDir string, addToRegistry bool) error {
 }
 
 func addToRegistryFile(org, repoName string) error {
-	regPath, err := repos.FindRegistry()
+	regPath, err := repos.FindRegistry(coreio.Local)
 	if err != nil {
 		return errors.New(i18n.T("cmd.pkg.error.no_repos_yaml"))
 	}
 
-	reg, err := repos.LoadRegistry(regPath)
+	reg, err := repos.LoadRegistry(coreio.Local, regPath)
 	if err != nil {
 		return err
 	}

internal/cmd/pkgcmd/cmd_manage.go

@@ -28,12 +28,12 @@ func addPkgListCommand(parent *cobra.Command) {
 }
 
 func runPkgList() error {
-	regPath, err := repos.FindRegistry()
+	regPath, err := repos.FindRegistry(coreio.Local)
 	if err != nil {
 		return errors.New(i18n.T("cmd.pkg.error.no_repos_yaml_workspace"))
 	}
 
-	reg, err := repos.LoadRegistry(regPath)
+	reg, err := repos.LoadRegistry(coreio.Local, regPath)
 	if err != nil {
 		return fmt.Errorf("%s: %w", i18n.T("i18n.fail.load", "registry"), err)
 	}
@@ -113,12 +113,12 @@ func addPkgUpdateCommand(parent *cobra.Command) {
 }
 
 func runPkgUpdate(packages []string, all bool) error {
-	regPath, err := repos.FindRegistry()
+	regPath, err := repos.FindRegistry(coreio.Local)
 	if err != nil {
 		return errors.New(i18n.T("cmd.pkg.error.no_repos_yaml"))
 	}
 
-	reg, err := repos.LoadRegistry(regPath)
+	reg, err := repos.LoadRegistry(coreio.Local, regPath)
 	if err != nil {
 		return fmt.Errorf("%s: %w", i18n.T("i18n.fail.load", "registry"), err)
 	}
@@ -193,12 +193,12 @@ func addPkgOutdatedCommand(parent *cobra.Command) {
 }
 
 func runPkgOutdated() error {
-	regPath, err := repos.FindRegistry()
+	regPath, err := repos.FindRegistry(coreio.Local)
 	if err != nil {
 		return errors.New(i18n.T("cmd.pkg.error.no_repos_yaml"))
 	}
 
-	reg, err := repos.LoadRegistry(regPath)
+	reg, err := repos.LoadRegistry(coreio.Local, regPath)
 	if err != nil {
 		return fmt.Errorf("%s: %w", i18n.T("i18n.fail.load", "registry"), err)
 	}

internal/cmd/pkgcmd/cmd_search.go

@@ -13,6 +13,7 @@ import (
 
 	"github.com/host-uk/core/pkg/cache"
 	"github.com/host-uk/core/pkg/i18n"
+	coreio "github.com/host-uk/core/pkg/io"
 	"github.com/host-uk/core/pkg/repos"
 	"github.com/spf13/cobra"
 )
@@ -69,7 +70,7 @@ type ghRepo struct {
 func runPkgSearch(org, pattern, repoType string, limit int, refresh bool) error {
 	// Initialize cache in workspace .core/ directory
 	var cacheDir string
-	if regPath, err := repos.FindRegistry(); err == nil {
+	if regPath, err := repos.FindRegistry(coreio.Local); err == nil {
 		cacheDir = filepath.Join(filepath.Dir(regPath), ".core", "cache")
 	}
 

internal/cmd/qa/cmd_health.go

@@ -14,6 +14,7 @@ import (
 
 	"github.com/host-uk/core/pkg/cli"
 	"github.com/host-uk/core/pkg/i18n"
+	"github.com/host-uk/core/pkg/io"
 	"github.com/host-uk/core/pkg/log"
 	"github.com/host-uk/core/pkg/repos"
 )
@@ -71,13 +72,13 @@ func runHealth() error {
 	var err error
 
 	if healthRegistry != "" {
-		reg, err = repos.LoadRegistry(healthRegistry)
+		reg, err = repos.LoadRegistry(io.Local, healthRegistry)
 	} else {
-		registryPath, findErr := repos.FindRegistry()
+		registryPath, findErr := repos.FindRegistry(io.Local)
 		if findErr != nil {
 			return log.E("qa.health", i18n.T("error.registry_not_found"), nil)
 		}
-		reg, err = repos.LoadRegistry(registryPath)
+		reg, err = repos.LoadRegistry(io.Local, registryPath)
 	}
 	if err != nil {
 		return log.E("qa.health", "failed to load registry", err)

internal/cmd/qa/cmd_issues.go

@@ -17,6 +17,7 @@ import (
 
 	"github.com/host-uk/core/pkg/cli"
 	"github.com/host-uk/core/pkg/i18n"
+	"github.com/host-uk/core/pkg/io"
 	"github.com/host-uk/core/pkg/log"
 	"github.com/host-uk/core/pkg/repos"
 )
@@ -100,13 +101,13 @@ func runQAIssues() error {
 	var err error
 
 	if issuesRegistry != "" {
-		reg, err = repos.LoadRegistry(issuesRegistry)
+		reg, err = repos.LoadRegistry(io.Local, issuesRegistry)
 	} else {
-		registryPath, findErr := repos.FindRegistry()
+		registryPath, findErr := repos.FindRegistry(io.Local)
 		if findErr != nil {
 			return log.E("qa.issues", i18n.T("error.registry_not_found"), nil)
 		}
-		reg, err = repos.LoadRegistry(registryPath)
+		reg, err = repos.LoadRegistry(io.Local, registryPath)
 	}
 	if err != nil {
 		return log.E("qa.issues", "failed to load registry", err)

internal/cmd/security/cmd_security.go

@@ -8,6 +8,7 @@ import (
 
 	"github.com/host-uk/core/pkg/cli"
 	"github.com/host-uk/core/pkg/i18n"
+	"github.com/host-uk/core/pkg/io"
 	"github.com/host-uk/core/pkg/repos"
 )
 
@@ -106,18 +107,18 @@ type SecretScanningAlert struct {
 // loadRegistry loads the repository registry.
 func loadRegistry(registryPath string) (*repos.Registry, error) {
 	if registryPath != "" {
-		reg, err := repos.LoadRegistry(registryPath)
+		reg, err := repos.LoadRegistry(io.Local, registryPath)
 		if err != nil {
 			return nil, cli.Wrap(err, "load registry")
 		}
 		return reg, nil
 	}
 
-	path, err := repos.FindRegistry()
+	path, err := repos.FindRegistry(io.Local)
 	if err != nil {
 		return nil, cli.Wrap(err, "find registry")
 	}
-	reg, err := repos.LoadRegistry(path)
+	reg, err := repos.LoadRegistry(io.Local, path)
 	if err != nil {
 		return nil, cli.Wrap(err, "load registry")
 	}

internal/cmd/setup/cmd_bootstrap.go

@@ -30,7 +30,7 @@ func runSetupOrchestrator(registryPath, only string, dryRun, all bool, projectNa
 	if registryPath != "" {
 		foundRegistry = registryPath
 	} else {
-		foundRegistry, err = repos.FindRegistry()
+		foundRegistry, err = repos.FindRegistry(coreio.Local)
 	}
 
 	// If registry exists, use registry mode
@@ -128,7 +128,7 @@ func runBootstrap(ctx context.Context, only string, dryRun, all bool, projectNam
 		return nil
 	}
 
-	reg, err := repos.LoadRegistry(registryPath)
+	reg, err := repos.LoadRegistry(coreio.Local, registryPath)
 	if err != nil {
 		return fmt.Errorf("failed to load registry from %s: %w", devopsRepo, err)
 	}

internal/cmd/setup/cmd_github.go

@@ -24,6 +24,7 @@ import (
 
 	"github.com/host-uk/core/pkg/cli"
 	"github.com/host-uk/core/pkg/i18n"
+	coreio "github.com/host-uk/core/pkg/io"
 	"github.com/host-uk/core/pkg/repos"
 	"github.com/spf13/cobra"
 )
@@ -78,12 +79,12 @@ func runGitHubSetup() error {
 	}
 
 	// Find registry
-	registryPath, err := repos.FindRegistry()
+	registryPath, err := repos.FindRegistry(coreio.Local)
 	if err != nil {
 		return cli.Wrap(err, i18n.T("error.registry_not_found"))
 	}
 
-	reg, err := repos.LoadRegistry(registryPath)
+	reg, err := repos.LoadRegistry(coreio.Local, registryPath)
 	if err != nil {
 		return cli.Wrap(err, "failed to load registry")
 	}

internal/cmd/setup/cmd_registry.go

@@ -22,7 +22,7 @@ import (
 
 // runRegistrySetup loads a registry from path and runs setup.
 func runRegistrySetup(ctx context.Context, registryPath, only string, dryRun, all, runBuild bool) error {
-	reg, err := repos.LoadRegistry(registryPath)
+	reg, err := repos.LoadRegistry(coreio.Local, registryPath)
 	if err != nil {
 		return fmt.Errorf("failed to load registry: %w", err)
 	}

pkg/cli/daemon.go

@@ -74,13 +74,14 @@ func IsStderrTTY() bool {
 
 // PIDFile manages a process ID file for single-instance enforcement.
 type PIDFile struct {
+	medium io.Medium
 	path   string
 	mu     sync.Mutex
 }
 
 // NewPIDFile creates a PID file manager.
-func NewPIDFile(path string) *PIDFile {
+func NewPIDFile(m io.Medium, path string) *PIDFile {
-	return &PIDFile{path: path}
+	return &PIDFile{medium: m, path: path}
 }
 
 // Acquire writes the current PID to the file.
@@ -90,7 +91,7 @@ func (p *PIDFile) Acquire() error {
 	defer p.mu.Unlock()
 
 	// Check if PID file exists
-	if data, err := io.Local.Read(p.path); err == nil {
+	if data, err := p.medium.Read(p.path); err == nil {
 		pid, err := strconv.Atoi(data)
 		if err == nil && pid > 0 {
 			// Check if process is still running
@@ -101,19 +102,19 @@ func (p *PIDFile) Acquire() error {
 			}
 		}
 		// Stale PID file, remove it
-		_ = io.Local.Delete(p.path)
+		_ = p.medium.Delete(p.path)
 	}
 
 	// Ensure directory exists
 	if dir := filepath.Dir(p.path); dir != "." {
-		if err := io.Local.EnsureDir(dir); err != nil {
+		if err := p.medium.EnsureDir(dir); err != nil {
 			return fmt.Errorf("failed to create PID directory: %w", err)
 		}
 	}
 
 	// Write current PID
 	pid := os.Getpid()
-	if err := io.Local.Write(p.path, strconv.Itoa(pid)); err != nil {
+	if err := p.medium.Write(p.path, strconv.Itoa(pid)); err != nil {
 		return fmt.Errorf("failed to write PID file: %w", err)
 	}
 
@@ -124,7 +125,7 @@ func (p *PIDFile) Acquire() error {
 func (p *PIDFile) Release() error {
 	p.mu.Lock()
 	defer p.mu.Unlock()
-	return io.Local.Delete(p.path)
+	return p.medium.Delete(p.path)
 }
 
 // Path returns the PID file path.
@@ -246,6 +247,10 @@ func (h *HealthServer) Addr() string {
 
 // DaemonOptions configures daemon mode execution.
 type DaemonOptions struct {
+	// Medium is the storage backend for PID files.
+	// Defaults to io.Local if not set.
+	Medium io.Medium
+
 	// PIDFile path for single-instance enforcement.
 	// Leave empty to skip PID file management.
 	PIDFile string
@@ -282,6 +287,9 @@ func NewDaemon(opts DaemonOptions) *Daemon {
 	if opts.ShutdownTimeout == 0 {
 		opts.ShutdownTimeout = 30 * time.Second
 	}
+	if opts.Medium == nil {
+		opts.Medium = io.Local
+	}
 
 	d := &Daemon{
 		opts:   opts,
@@ -289,7 +297,7 @@ func NewDaemon(opts DaemonOptions) *Daemon {
 	}
 
 	if opts.PIDFile != "" {
-		d.pid = NewPIDFile(opts.PIDFile)
+		d.pid = NewPIDFile(opts.Medium, opts.PIDFile)
 	}
 
 	if opts.HealthAddr != "" {

pkg/cli/daemon_test.go

@@ -3,11 +3,10 @@ package cli
 import (
 	"context"
 	"net/http"
-	"os"
-	"path/filepath"
 	"testing"
 	"time"
 
+	"github.com/host-uk/core/pkg/io"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
 )
@@ -28,37 +27,36 @@ func TestDetectMode(t *testing.T) {
 
 func TestPIDFile(t *testing.T) {
 	t.Run("acquire and release", func(t *testing.T) {
-		tmpDir := t.TempDir()
+		m := io.NewMockMedium()
-		pidPath := filepath.Join(tmpDir, "test.pid")
+		pidPath := "/tmp/test.pid"
 
-		pid := NewPIDFile(pidPath)
+		pid := NewPIDFile(m, pidPath)
 
 		// Acquire should succeed
 		err := pid.Acquire()
 		require.NoError(t, err)
 
 		// File should exist with our PID
-		data, err := os.ReadFile(pidPath)
+		data, err := m.Read(pidPath)
 		require.NoError(t, err)
-		assert.Contains(t, string(data), "")
+		assert.NotEmpty(t, data)
 
 		// Release should remove file
 		err = pid.Release()
 		require.NoError(t, err)
 
-		_, err = os.Stat(pidPath)
+		assert.False(t, m.Exists(pidPath))
-		assert.True(t, os.IsNotExist(err))
 	})
 
 	t.Run("stale pid file", func(t *testing.T) {
-		tmpDir := t.TempDir()
+		m := io.NewMockMedium()
-		pidPath := filepath.Join(tmpDir, "stale.pid")
+		pidPath := "/tmp/stale.pid"
 
 		// Write a stale PID (non-existent process)
-		err := os.WriteFile(pidPath, []byte("999999999"), 0644)
+		err := m.Write(pidPath, "999999999")
 		require.NoError(t, err)
 
-		pid := NewPIDFile(pidPath)
+		pid := NewPIDFile(m, pidPath)
 
 		// Should acquire successfully (stale PID removed)
 		err = pid.Acquire()
@@ -69,23 +67,23 @@ func TestPIDFile(t *testing.T) {
 	})
 
 	t.Run("creates parent directory", func(t *testing.T) {
-		tmpDir := t.TempDir()
+		m := io.NewMockMedium()
-		pidPath := filepath.Join(tmpDir, "subdir", "nested", "test.pid")
+		pidPath := "/tmp/subdir/nested/test.pid"
 
-		pid := NewPIDFile(pidPath)
+		pid := NewPIDFile(m, pidPath)
 
 		err := pid.Acquire()
 		require.NoError(t, err)
 
-		_, err = os.Stat(pidPath)
+		assert.True(t, m.Exists(pidPath))
-		require.NoError(t, err)
 
 		err = pid.Release()
 		require.NoError(t, err)
 	})
 
 	t.Run("path getter", func(t *testing.T) {
-		pid := NewPIDFile("/tmp/test.pid")
+		m := io.NewMockMedium()
+		pid := NewPIDFile(m, "/tmp/test.pid")
 		assert.Equal(t, "/tmp/test.pid", pid.Path())
 	})
 }
@@ -157,10 +155,12 @@ func TestHealthServer(t *testing.T) {
 
 func TestDaemon(t *testing.T) {
 	t.Run("start and stop", func(t *testing.T) {
-		tmpDir := t.TempDir()
+		m := io.NewMockMedium()
+		pidPath := "/tmp/test.pid"
 
 		d := NewDaemon(DaemonOptions{
-			PIDFile:         filepath.Join(tmpDir, "test.pid"),
+			Medium:          m,
+			PIDFile:         pidPath,
 			HealthAddr:      "127.0.0.1:0",
 			ShutdownTimeout: 5 * time.Second,
 		})
@@ -182,8 +182,7 @@ func TestDaemon(t *testing.T) {
 		require.NoError(t, err)
 
 		// PID file should be removed
-		_, err = os.Stat(filepath.Join(tmpDir, "test.pid"))
+		assert.False(t, m.Exists(pidPath))
-		assert.True(t, os.IsNotExist(err))
 	})
 
 	t.Run("double start fails", func(t *testing.T) {

pkg/container/linuxkit.go

@@ -235,6 +235,9 @@ func (m *LinuxKitManager) waitForExit(id string, cmd *exec.Cmd) {
 
 // Stop stops a running container by sending SIGTERM.
 func (m *LinuxKitManager) Stop(ctx context.Context, id string) error {
+	if err := ctx.Err(); err != nil {
+		return err
+	}
 	container, ok := m.state.Get(id)
 	if !ok {
 		return fmt.Errorf("container not found: %s", id)
@@ -293,6 +296,9 @@ func (m *LinuxKitManager) Stop(ctx context.Context, id string) error {
 
 // List returns all known containers, verifying process state.
 func (m *LinuxKitManager) List(ctx context.Context) ([]*Container, error) {
+	if err := ctx.Err(); err != nil {
+		return nil, err
+	}
 	containers := m.state.All()
 
 	// Verify each running container's process is still alive
@@ -322,6 +328,9 @@ func isProcessRunning(pid int) bool {
 
 // Logs returns a reader for the container's log output.
 func (m *LinuxKitManager) Logs(ctx context.Context, id string, follow bool) (goio.ReadCloser, error) {
+	if err := ctx.Err(); err != nil {
+		return nil, err
+	}
 	_, ok := m.state.Get(id)
 	if !ok {
 		return nil, fmt.Errorf("container not found: %s", id)
@@ -409,6 +418,9 @@ func (f *followReader) Close() error {
 
 // Exec executes a command inside the container via SSH.
 func (m *LinuxKitManager) Exec(ctx context.Context, id string, cmd []string) error {
+	if err := ctx.Err(); err != nil {
+		return err
+	}
 	container, ok := m.state.Get(id)
 	if !ok {
 		return fmt.Errorf("container not found: %s", id)

pkg/repos/registry.go

@@ -20,6 +20,7 @@ type Registry struct {
 	BasePath string           `yaml:"base_path"`
 	Repos    map[string]*Repo `yaml:"repos"`
 	Defaults RegistryDefaults `yaml:"defaults"`
+	medium   io.Medium        `yaml:"-"`
 }
 
 // RegistryDefaults contains default values applied to all repos.
@@ -57,16 +58,13 @@ type Repo struct {
 
 	// Computed fields
 	Path     string    `yaml:"-"` // Full path to repo directory
+	registry *Registry `yaml:"-"`
 }
 
-// LoadRegistry reads and parses a repos.yaml file.
+// LoadRegistry reads and parses a repos.yaml file from the given medium.
-func LoadRegistry(path string) (*Registry, error) {
+// The path should be a valid path for the provided medium.
-	absPath, err := filepath.Abs(path)
+func LoadRegistry(m io.Medium, path string) (*Registry, error) {
-	if err != nil {
+	content, err := m.Read(path)
-		return nil, fmt.Errorf("failed to resolve path: %w", err)
-	}
-
-	content, err := io.Local.Read(absPath)
 	if err != nil {
 		return nil, fmt.Errorf("failed to read registry file: %w", err)
 	}
@@ -77,6 +75,8 @@ func LoadRegistry(path string) (*Registry, error) {
 		return nil, fmt.Errorf("failed to parse registry file: %w", err)
 	}
 
+	reg.medium = m
+
 	// Expand base path
 	reg.BasePath = expandPath(reg.BasePath)
 
@@ -84,6 +84,7 @@ func LoadRegistry(path string) (*Registry, error) {
 	for name, repo := range reg.Repos {
 		repo.Name = name
 		repo.Path = filepath.Join(reg.BasePath, name)
+		repo.registry = &reg
 
 		// Apply defaults if not set
 		if repo.CI == "" {
@@ -96,7 +97,8 @@ func LoadRegistry(path string) (*Registry, error) {
 
 // FindRegistry searches for repos.yaml in common locations.
 // It checks: current directory, parent directories, and home directory.
-func FindRegistry() (string, error) {
+// This function is primarily intended for use with io.Local or other local-like filesystems.
+func FindRegistry(m io.Medium) (string, error) {
 	// Check current directory and parents
 	dir, err := os.Getwd()
 	if err != nil {
@@ -105,7 +107,7 @@ func FindRegistry() (string, error) {
 
 	for {
 		candidate := filepath.Join(dir, "repos.yaml")
-		if io.Local.Exists(candidate) {
+		if m.Exists(candidate) {
 			return candidate, nil
 		}
 
@@ -128,7 +130,7 @@ func FindRegistry() (string, error) {
 	}
 
 	for _, p := range commonPaths {
-		if io.Local.Exists(p) {
+		if m.Exists(p) {
 			return p, nil
 		}
 	}
@@ -138,21 +140,18 @@ func FindRegistry() (string, error) {
 
 // ScanDirectory creates a Registry by scanning a directory for git repos.
 // This is used as a fallback when no repos.yaml is found.
-func ScanDirectory(dir string) (*Registry, error) {
+// The dir should be a valid path for the provided medium.
-	absDir, err := filepath.Abs(dir)
+func ScanDirectory(m io.Medium, dir string) (*Registry, error) {
-	if err != nil {
+	entries, err := m.List(dir)
-		return nil, fmt.Errorf("failed to resolve directory path: %w", err)
-	}
-
-	entries, err := io.Local.List(absDir)
 	if err != nil {
 		return nil, fmt.Errorf("failed to read directory: %w", err)
 	}
 
 	reg := &Registry{
 		Version:  1,
-		BasePath: absDir,
+		BasePath: dir,
 		Repos:    make(map[string]*Repo),
+		medium:   m,
 	}
 
 	// Try to detect org from git remote
@@ -161,10 +160,10 @@ func ScanDirectory(dir string) (*Registry, error) {
 			continue
 		}
 
-		repoPath := filepath.Join(absDir, entry.Name())
+		repoPath := filepath.Join(dir, entry.Name())
 		gitPath := filepath.Join(repoPath, ".git")
 
-		if !io.Local.IsDir(gitPath) {
+		if !m.IsDir(gitPath) {
 			continue // Not a git repo
 		}
 
@@ -172,13 +171,14 @@ func ScanDirectory(dir string) (*Registry, error) {
 			Name:     entry.Name(),
 			Path:     repoPath,
 			Type:     "module", // Default type
+			registry: reg,
 		}
 
 		reg.Repos[entry.Name()] = repo
 
 		// Try to detect org from first repo's remote
 		if reg.Org == "" {
-			reg.Org = detectOrg(repoPath)
+			reg.Org = detectOrg(m, repoPath)
 		}
 	}
 
@@ -186,10 +186,10 @@ func ScanDirectory(dir string) (*Registry, error) {
 }
 
 // detectOrg tries to extract the GitHub org from a repo's origin remote.
-func detectOrg(repoPath string) string {
+func detectOrg(m io.Medium, repoPath string) string {
 	// Try to read git remote
 	configPath := filepath.Join(repoPath, ".git", "config")
-	content, err := io.Local.Read(configPath)
+	content, err := m.Read(configPath)
 	if err != nil {
 		return ""
 	}
@@ -301,13 +301,20 @@ func (r *Registry) TopologicalOrder() ([]*Repo, error) {
 
 // Exists checks if the repo directory exists on disk.
 func (repo *Repo) Exists() bool {
-	return io.Local.IsDir(repo.Path)
+	return repo.getMedium().IsDir(repo.Path)
 }
 
 // IsGitRepo checks if the repo directory contains a .git folder.
 func (repo *Repo) IsGitRepo() bool {
 	gitPath := filepath.Join(repo.Path, ".git")
-	return io.Local.IsDir(gitPath)
+	return repo.getMedium().IsDir(gitPath)
+}
+
+func (repo *Repo) getMedium() io.Medium {
+	if repo.registry != nil && repo.registry.medium != nil {
+		return repo.registry.medium
+	}
+	return io.Local
 }
 
 // expandPath expands ~ to home directory.

pkg/repos/registry_test.go

@@ -0,0 +1,77 @@
+package repos
+
+import (
+	"testing"
+
+	"github.com/host-uk/core/pkg/io"
+	"github.com/stretchr/testify/assert"
+)
+
+func TestLoadRegistry(t *testing.T) {
+	m := io.NewMockMedium()
+	yaml := `
+version: 1
+org: host-uk
+base_path: /tmp/repos
+repos:
+  core:
+    type: foundation
+    description: Core package
+`
+	_ = m.Write("/tmp/repos.yaml", yaml)
+
+	reg, err := LoadRegistry(m, "/tmp/repos.yaml")
+	assert.NoError(t, err)
+	assert.NotNil(t, reg)
+	assert.Equal(t, "host-uk", reg.Org)
+	assert.Equal(t, "/tmp/repos", reg.BasePath)
+	assert.Equal(t, m, reg.medium)
+
+	repo, ok := reg.Get("core")
+	assert.True(t, ok)
+	assert.Equal(t, "core", repo.Name)
+	assert.Equal(t, "/tmp/repos/core", repo.Path)
+	assert.Equal(t, reg, repo.registry)
+}
+
+func TestRepo_Exists(t *testing.T) {
+	m := io.NewMockMedium()
+	reg := &Registry{
+		medium:   m,
+		BasePath: "/tmp/repos",
+		Repos:    make(map[string]*Repo),
+	}
+	repo := &Repo{
+		Name:     "core",
+		Path:     "/tmp/repos/core",
+		registry: reg,
+	}
+
+	// Not exists yet
+	assert.False(t, repo.Exists())
+
+	// Create directory in mock
+	_ = m.EnsureDir("/tmp/repos/core")
+	assert.True(t, repo.Exists())
+}
+
+func TestRepo_IsGitRepo(t *testing.T) {
+	m := io.NewMockMedium()
+	reg := &Registry{
+		medium:   m,
+		BasePath: "/tmp/repos",
+		Repos:    make(map[string]*Repo),
+	}
+	repo := &Repo{
+		Name:     "core",
+		Path:     "/tmp/repos/core",
+		registry: reg,
+	}
+
+	// Not a git repo yet
+	assert.False(t, repo.IsGitRepo())
+
+	// Create .git directory in mock
+	_ = m.EnsureDir("/tmp/repos/core/.git")
+	assert.True(t, repo.IsGitRepo())
+}