fix(apply): propagate read errors, auto-open repo, dedupe adapter base (#6)

Three robustness fixes for the apply pipeline:

1. Silent read errors on state/target files treated 'file absent' as
   'file empty' and fast-forward-overwrote user edits. Add
   common.ReadExistingFile that returns (nil,nil) only on
   os.IsNotExist; other I/O errors propagate. Use it from apply.Run
   and from every adapter's Render (claudecode, crush, kilo,
   opencode, goose, zed).

2. apply.Run required callers to pre-construct *gitx.Repo; passing
   nil silently skipped the commit. Run now auto-opens a repo from
   Bundle.Root, gracefully no-ops when the root is not a git repo,
   and uses a new gitx.HasStagedChanges() check to skip the no-op
   'nothing to commit' that triggered the original silent-skip.

3. Each of 7 adapter packages re-implemented the same 25-line
   Option/WithHome/New constructor. Hoist into adapter.Base +
   adapter.BaseOption + NewBase. Each adapter embeds *Base and
   reduces to a 9-line constructor. Public New(WithHome(h)) API
   preserved; a.home becomes a.Home.

Tests:
  - apply: 5 new (propagates-read-error, auto-opens-repo,
    no-repo-skips-commit, skips-no-op-commit, commit-message-counts)
  - gitx: 2 new (HasStagedChanges empty/after-add)
  - adapter/common: 3 new (ReadExistingFile missing/content/perm)
  - adapter: 4 new (NewBase default/WithHome/order/typed)
  - existing adapter tests unchanged — verify a.Home still honoured.

internal/adapters/cagent/cagent.go

@@ -19,21 +19,16 @@ import (
 const name = "cagent"
 
 // Adapter implements adapter.Adapter for the cagent harness.
-type Adapter struct{ home string }
+type Adapter struct {
+	*adapter.Base
+}
 
-// Option configures an Adapter.
-type Option func(*Adapter)
-
-// WithHome overrides the home directory (defaults to os.UserHomeDir).
-func WithHome(h string) Option { return func(a *Adapter) { a.home = h } }
+// WithHome overrides the home directory used to resolve target paths.
+func WithHome(h string) adapter.BaseOption { return func(b *adapter.Base) { b.Home = h } }
 
 // New returns a new Adapter with the given options applied.
-func New(opts ...Option) *Adapter {
-	a := &Adapter{home: common.DefaultHome()}
-	for _, o := range opts {
-		o(a)
-	}
-	return a
+func New(opts ...adapter.BaseOption) *Adapter {
+	return &Adapter{Base: adapter.NewBase(opts...)}
 }
 
 // Name returns the harness identifier.
@@ -53,14 +48,14 @@ func (a *Adapter) Capabilities() adapter.HarnessCapabilities {
 
 // Detect returns true when ~/.config/cagent/ exists.
 func (a *Adapter) Detect() bool {
-	_, err := os.Stat(filepath.Join(a.home, ".config", "cagent"))
+	_, err := os.Stat(filepath.Join(a.Home, ".config", "cagent"))
 	return err == nil
 }
 
 // Render produces a starter default.yaml for cagent.
 func (a *Adapter) Render(b *canonical.Bundle) (*adapter.FileSet, error) {
 	fs := adapter.NewFileSet()
-	cfgPath := filepath.Join(a.home, ".config", "cagent", "default.yaml")
+	cfgPath := filepath.Join(a.Home, ".config", "cagent", "default.yaml")
 
 	instructions := b.Instructions.Global
 	if override, ok := b.Instructions.PerHarness[name]; ok && override != "" {

internal/adapters/claudecode/claudecode.go

@@ -2,6 +2,7 @@
 package claudecode
 
 import (
+	"fmt"
 	"os"
 	"path/filepath"
 
@@ -14,22 +15,15 @@ const name = "claude-code"
 
 // Adapter implements adapter.Adapter for the claude-code harness.
 type Adapter struct {
-	home string
+	*adapter.Base
 }
 
-// Option configures an Adapter.
-type Option func(*Adapter)
-
-// WithHome overrides the home directory (defaults to os.UserHomeDir).
-func WithHome(h string) Option { return func(a *Adapter) { a.home = h } }
+// WithHome overrides the home directory used to resolve target paths.
+func WithHome(h string) adapter.BaseOption { return func(b *adapter.Base) { b.Home = h } }
 
 // New returns a new Adapter with the given options applied.
-func New(opts ...Option) *Adapter {
-	a := &Adapter{home: common.DefaultHome()}
-	for _, o := range opts {
-		o(a)
-	}
-	return a
+func New(opts ...adapter.BaseOption) *Adapter {
+	return &Adapter{Base: adapter.NewBase(opts...)}
 }
 
 // Name returns the harness identifier.
@@ -50,7 +44,7 @@ func (a *Adapter) Capabilities() adapter.HarnessCapabilities {
 
 // Detect returns true when ~/.claude exists.
 func (a *Adapter) Detect() bool {
-	_, err := os.Stat(filepath.Join(a.home, ".claude"))
+	_, err := os.Stat(filepath.Join(a.Home, ".claude"))
 	return err == nil
 }
 
@@ -59,7 +53,7 @@ func (a *Adapter) Detect() bool {
 // only manages skills/agents symlinks, CLAUDE.md, and MCP servers.
 func (a *Adapter) Render(b *canonical.Bundle) (*adapter.FileSet, error) {
 	fs := adapter.NewFileSet()
-	base := filepath.Join(a.home, ".claude")
+	base := filepath.Join(a.Home, ".claude")
 
 	fs.Add(adapter.File{
 		Dest:          filepath.Join(base, "skills"),
@@ -92,7 +86,10 @@ func (a *Adapter) Render(b *canonical.Bundle) (*adapter.FileSet, error) {
 	overlay := map[string]any{"mcpServers": mcpMap}
 
 	dedicatedPath := filepath.Join(base, "mcp_servers.json")
-	dedicatedExisting, _ := os.ReadFile(dedicatedPath)
+	dedicatedExisting, err := common.ReadExistingFile(dedicatedPath)
+	if err != nil {
+		return nil, fmt.Errorf("read %s: %w", dedicatedPath, err)
+	}
 	dedicatedMerged, err := common.MergeJSONKeys(dedicatedExisting, overlay)
 	if err != nil {
 		return nil, err
@@ -103,9 +100,12 @@ func (a *Adapter) Render(b *canonical.Bundle) (*adapter.FileSet, error) {
 		Content: dedicatedMerged,
 	})
 
-	livePath := filepath.Join(a.home, ".claude.json")
+	livePath := filepath.Join(a.Home, ".claude.json")
 	if _, err := os.Stat(livePath); err == nil {
-		liveExisting, _ := os.ReadFile(livePath)
+		liveExisting, err := common.ReadExistingFile(livePath)
+		if err != nil {
+			return nil, fmt.Errorf("read %s: %w", livePath, err)
+		}
 		liveMerged, err := common.MergeJSONKeys(liveExisting, overlay)
 		if err != nil {
 			return nil, err

internal/adapters/crush/crush.go

@@ -2,6 +2,7 @@
 package crush
 
 import (
+	"fmt"
 	"os"
 	"path/filepath"
 
@@ -13,21 +14,16 @@ import (
 const name = "crush"
 
 // Adapter implements adapter.Adapter for the crush harness.
-type Adapter struct{ home string }
+type Adapter struct {
+	*adapter.Base
+}
 
-// Option configures an Adapter.
-type Option func(*Adapter)
-
-// WithHome overrides the home directory (defaults to os.UserHomeDir).
-func WithHome(h string) Option { return func(a *Adapter) { a.home = h } }
+// WithHome overrides the home directory used to resolve target paths.
+func WithHome(h string) adapter.BaseOption { return func(b *adapter.Base) { b.Home = h } }
 
 // New returns a new Adapter with the given options applied.
-func New(opts ...Option) *Adapter {
-	a := &Adapter{home: common.DefaultHome()}
-	for _, o := range opts {
-		o(a)
-	}
-	return a
+func New(opts ...adapter.BaseOption) *Adapter {
+	return &Adapter{Base: adapter.NewBase(opts...)}
 }
 
 // Name returns the harness identifier.
@@ -47,7 +43,7 @@ func (a *Adapter) Capabilities() adapter.HarnessCapabilities {
 
 // Detect returns true when ~/.config/crush exists.
 func (a *Adapter) Detect() bool {
-	_, err := os.Stat(filepath.Join(a.home, ".config", "crush"))
+	_, err := os.Stat(filepath.Join(a.Home, ".config", "crush"))
 	return err == nil
 }
 
@@ -56,7 +52,7 @@ func (a *Adapter) Detect() bool {
 // MCP key is "mcp" (not "mcpServers"); entries include a "type" field.
 func (a *Adapter) Render(b *canonical.Bundle) (*adapter.FileSet, error) {
 	fs := adapter.NewFileSet()
-	base := filepath.Join(a.home, ".config", "crush")
+	base := filepath.Join(a.Home, ".config", "crush")
 
 	fs.Add(adapter.File{
 		Dest:          filepath.Join(base, "skills"),
@@ -65,7 +61,10 @@ func (a *Adapter) Render(b *canonical.Bundle) (*adapter.FileSet, error) {
 	})
 
 	cfgPath := filepath.Join(base, "crush.json")
-	existing, _ := os.ReadFile(cfgPath)
+	existing, err := common.ReadExistingFile(cfgPath)
+	if err != nil {
+		return nil, fmt.Errorf("read %s: %w", cfgPath, err)
+	}
 	overlay := map[string]any{}
 	if providers := common.ProvidersAsCrushMap(&b.Profile); len(providers) > 0 {
 		overlay["providers"] = providers

internal/adapters/goose/goose.go

@@ -10,6 +10,7 @@
 package goose
 
 import (
+	"fmt"
 	"os"
 	"path/filepath"
 	"strings"
@@ -22,21 +23,16 @@ import (
 const name = "goose"
 
 // Adapter implements adapter.Adapter for the Goose harness.
-type Adapter struct{ home string }
+type Adapter struct {
+	*adapter.Base
+}
 
-// Option configures an Adapter.
-type Option func(*Adapter)
-
-// WithHome overrides the home directory (defaults to os.UserHomeDir).
-func WithHome(h string) Option { return func(a *Adapter) { a.home = h } }
+// WithHome overrides the home directory used to resolve target paths.
+func WithHome(h string) adapter.BaseOption { return func(b *adapter.Base) { b.Home = h } }
 
 // New returns a new Adapter with the given options applied.
-func New(opts ...Option) *Adapter {
-	a := &Adapter{home: common.DefaultHome()}
-	for _, o := range opts {
-		o(a)
-	}
-	return a
+func New(opts ...adapter.BaseOption) *Adapter {
+	return &Adapter{Base: adapter.NewBase(opts...)}
 }
 
 // Name returns the harness identifier.
@@ -56,7 +52,7 @@ func (a *Adapter) Capabilities() adapter.HarnessCapabilities {
 
 // Detect returns true when ~/.config/goose/ exists.
 func (a *Adapter) Detect() bool {
-	_, err := os.Stat(filepath.Join(a.home, ".config", "goose"))
+	_, err := os.Stat(filepath.Join(a.Home, ".config", "goose"))
 	return err == nil
 }
 
@@ -67,23 +63,26 @@ func (a *Adapter) Detect() bool {
 // also added to the FileSet so goose can load the provider on first run.
 func (a *Adapter) Render(b *canonical.Bundle) (*adapter.FileSet, error) {
 	fs := adapter.NewFileSet()
-	cfgPath := filepath.Join(a.home, ".config", "goose", "config.yaml")
+	cfgPath := filepath.Join(a.Home, ".config", "goose", "config.yaml")
 
 	// goose reads skills from ~/.agents/skills/<name>/SKILL.md (open Agent Skills spec)
 	fs.Add(adapter.File{
-		Dest:          filepath.Join(a.home, ".agents", "skills"),
+		Dest:          filepath.Join(a.Home, ".agents", "skills"),
 		Kind:          adapter.SymlinkDir,
 		SymlinkTarget: filepath.Join(b.Root, "skills"),
 	})
 
-	existing, _ := os.ReadFile(cfgPath)
+	existing, err := common.ReadExistingFile(cfgPath)
+	if err != nil {
+		return nil, fmt.Errorf("read %s: %w", cfgPath, err)
+	}
 
 	provider, model := splitProviderModel(b.Profile.Gateway.DefaultModel)
 	if b.Profile.Gateway.URL != "" {
 		// Emit the custom provider JSON file.
 		body, providerName := common.GooseCustomProviderFile(&b.Profile)
 		if body != nil {
-			cpDir := filepath.Join(a.home, ".config", "goose", "custom_providers")
+			cpDir := filepath.Join(a.Home, ".config", "goose", "custom_providers")
 			fs.Add(adapter.File{
 				Dest:    filepath.Join(cpDir, providerName+".json"),
 				Kind:    adapter.RenderedFile,

internal/adapters/kilo/kilo.go

@@ -3,6 +3,7 @@ package kilo
 
 import (
 	"encoding/json"
+	"fmt"
 	"maps"
 	"os"
 	"path/filepath"
@@ -16,22 +17,15 @@ const name = "kilo"
 
 // Adapter implements adapter.Adapter for the kilo harness.
 type Adapter struct {
-	home string
+	*adapter.Base
 }
 
-// Option configures an Adapter.
-type Option func(*Adapter)
-
-// WithHome overrides the home directory (defaults to os.UserHomeDir).
-func WithHome(h string) Option { return func(a *Adapter) { a.home = h } }
+// WithHome overrides the home directory used to resolve target paths.
+func WithHome(h string) adapter.BaseOption { return func(b *adapter.Base) { b.Home = h } }
 
 // New returns a new Adapter with the given options applied.
-func New(opts ...Option) *Adapter {
-	a := &Adapter{home: common.DefaultHome()}
-	for _, o := range opts {
-		o(a)
-	}
-	return a
+func New(opts ...adapter.BaseOption) *Adapter {
+	return &Adapter{Base: adapter.NewBase(opts...)}
 }
 
 // Name returns the harness identifier.
@@ -51,7 +45,7 @@ func (a *Adapter) Capabilities() adapter.HarnessCapabilities {
 
 // Detect returns true when ~/.config/kilo exists.
 func (a *Adapter) Detect() bool {
-	_, err := os.Stat(filepath.Join(a.home, ".config", "kilo"))
+	_, err := os.Stat(filepath.Join(a.Home, ".config", "kilo"))
 	return err == nil
 }
 
@@ -62,7 +56,7 @@ func (a *Adapter) Detect() bool {
 // No "providers" key — kilo has no such concept.
 func (a *Adapter) Render(b *canonical.Bundle) (*adapter.FileSet, error) {
 	fs := adapter.NewFileSet()
-	base := filepath.Join(a.home, ".config", "kilo")
+	base := filepath.Join(a.Home, ".config", "kilo")
 
 	fs.Add(adapter.File{
 		Dest:          filepath.Join(base, "agent"),
@@ -71,13 +65,16 @@ func (a *Adapter) Render(b *canonical.Bundle) (*adapter.FileSet, error) {
 	})
 	// kilo reads skills from ~/.kilo/skills/<name>/SKILL.md
 	fs.Add(adapter.File{
-		Dest:          filepath.Join(a.home, ".kilo", "skills"),
+		Dest:          filepath.Join(a.Home, ".kilo", "skills"),
 		Kind:          adapter.SymlinkDir,
 		SymlinkTarget: filepath.Join(b.Root, "skills"),
 	})
 
 	cfgPath := filepath.Join(base, "kilo.json")
-	existing, _ := os.ReadFile(cfgPath)
+	existing, err := common.ReadExistingFile(cfgPath)
+	if err != nil {
+		return nil, fmt.Errorf("read %s: %w", cfgPath, err)
+	}
 	modelStr := common.KiloModelString(&b.Profile)
 	overlay := map[string]any{}
 	if providers := common.ProvidersAsMap(&b.Profile); len(providers) > 0 {

internal/adapters/opencode/opencode.go

@@ -3,6 +3,7 @@ package opencode
 
 import (
 	"encoding/json"
+	"fmt"
 	"os"
 	"path/filepath"
 
@@ -14,21 +15,16 @@ import (
 const name = "opencode"
 
 // Adapter implements adapter.Adapter for the opencode harness.
-type Adapter struct{ home string }
+type Adapter struct {
+	*adapter.Base
+}
 
-// Option configures an Adapter.
-type Option func(*Adapter)
-
-// WithHome overrides the home directory (defaults to os.UserHomeDir).
-func WithHome(h string) Option { return func(a *Adapter) { a.home = h } }
+// WithHome overrides the home directory used to resolve target paths.
+func WithHome(h string) adapter.BaseOption { return func(b *adapter.Base) { b.Home = h } }
 
 // New returns a new Adapter with the given options applied.
-func New(opts ...Option) *Adapter {
-	a := &Adapter{home: common.DefaultHome()}
-	for _, o := range opts {
-		o(a)
-	}
-	return a
+func New(opts ...adapter.BaseOption) *Adapter {
+	return &Adapter{Base: adapter.NewBase(opts...)}
 }
 
 // Name returns the harness identifier.
@@ -48,7 +44,7 @@ func (a *Adapter) Capabilities() adapter.HarnessCapabilities {
 
 // Detect returns true when ~/.config/opencode exists.
 func (a *Adapter) Detect() bool {
-	_, err := os.Stat(filepath.Join(a.home, ".config", "opencode"))
+	_, err := os.Stat(filepath.Join(a.Home, ".config", "opencode"))
 	return err == nil
 }
 
@@ -58,7 +54,7 @@ func (a *Adapter) Detect() bool {
 // "mcp" (map with type: local|remote entries).
 func (a *Adapter) Render(b *canonical.Bundle) (*adapter.FileSet, error) {
 	fs := adapter.NewFileSet()
-	base := filepath.Join(a.home, ".config", "opencode")
+	base := filepath.Join(a.Home, ".config", "opencode")
 
 	// opencode reads skills from ~/.config/opencode/skills/<name>/SKILL.md
 	fs.Add(adapter.File{
@@ -68,7 +64,10 @@ func (a *Adapter) Render(b *canonical.Bundle) (*adapter.FileSet, error) {
 	})
 
 	cfgPath := filepath.Join(base, "opencode.jsonc")
-	existing, _ := os.ReadFile(cfgPath)
+	existing, err := common.ReadExistingFile(cfgPath)
+	if err != nil {
+		return nil, fmt.Errorf("read %s: %w", cfgPath, err)
+	}
 
 	// Build the provider map, then absorb any existing providers at the same
 	// gateway URL so duplicates don't accumulate across apply runs.

internal/adapters/zed/zed.go

@@ -7,6 +7,7 @@ package zed
 
 import (
 	"encoding/json"
+	"fmt"
 	"os"
 	"path/filepath"
 
@@ -18,21 +19,16 @@ import (
 const name = "zed"
 
 // Adapter implements adapter.Adapter for the Zed harness.
-type Adapter struct{ home string }
+type Adapter struct {
+	*adapter.Base
+}
 
-// Option configures an Adapter.
-type Option func(*Adapter)
-
-// WithHome overrides the home directory (defaults to os.UserHomeDir).
-func WithHome(h string) Option { return func(a *Adapter) { a.home = h } }
+// WithHome overrides the home directory used to resolve target paths.
+func WithHome(h string) adapter.BaseOption { return func(b *adapter.Base) { b.Home = h } }
 
 // New returns a new Adapter with the given options applied.
-func New(opts ...Option) *Adapter {
-	a := &Adapter{home: common.DefaultHome()}
-	for _, o := range opts {
-		o(a)
-	}
-	return a
+func New(opts ...adapter.BaseOption) *Adapter {
+	return &Adapter{Base: adapter.NewBase(opts...)}
 }
 
 // Name returns the harness identifier.
@@ -53,7 +49,7 @@ func (a *Adapter) Capabilities() adapter.HarnessCapabilities {
 
 // Detect returns true when ~/.config/zed/ exists.
 func (a *Adapter) Detect() bool {
-	_, err := os.Stat(filepath.Join(a.home, ".config", "zed"))
+	_, err := os.Stat(filepath.Join(a.Home, ".config", "zed"))
 	return err == nil
 }
 
@@ -68,8 +64,11 @@ func (a *Adapter) Detect() bool {
 // pre-existing parse errors from user-configured entries.
 func (a *Adapter) Render(b *canonical.Bundle) (*adapter.FileSet, error) {
 	fs := adapter.NewFileSet()
-	cfgPath := filepath.Join(a.home, ".config", "zed", "settings.json")
-	existing, _ := os.ReadFile(cfgPath)
+	cfgPath := filepath.Join(a.Home, ".config", "zed", "settings.json")
+	existing, err := common.ReadExistingFile(cfgPath)
+	if err != nil {
+		return nil, fmt.Errorf("read %s: %w", cfgPath, err)
+	}
 
 	// Set context_servers to nil so MergeJSONKeys removes the key entirely,
 	// clearing any entries that trigger the serde ContextServerSettingsContent bug.