diff --git a/internal/cli/config.go b/internal/cli/config.go
index f38d406..dbac125 100644
--- a/internal/cli/config.go
+++ b/internal/cli/config.go
@@ -60,9 +60,11 @@ func runConfig(cmd *cobra.Command, local bool, explicitPath string) error {
 		return fmt.Errorf("no configuration found at %s; run 'skill-sync init' to create one", configPath)
 	}
 
+	// Agent directories live under the user home, not under the user config
+	// directory. These two lookups must stay separate.
 	d := discovery.New()
 	d.Getwd = getWd
-	d.UserHomeDir = func() (string, error) { return getUserConfig() }
+	d.UserHomeDir = getUserHome
 
 	discovered, err := d.Scan()
 	if err != nil {
diff --git a/internal/cli/config_test.go b/internal/cli/config_test.go
index b3f6282..caa122d 100644
--- a/internal/cli/config_test.go
+++ b/internal/cli/config_test.go
@@ -11,11 +11,19 @@ import (
 func TestConfigCmd(t *testing.T) {
 	origGetWd := getWd
 	origGetUserConfig := getUserConfig
+	origGetUserHome := getUserHome
 	defer func() {
 		getWd = origGetWd
 		getUserConfig = origGetUserConfig
+		getUserHome = origGetUserHome
 	}()
 
+	// Pin the home seam to an empty directory so these cases never discover the
+	// developer's real agent directories. Global discovery has dedicated
+	// coverage in TestConfigDiscoversGlobalAgents.
+	emptyHome := t.TempDir()
+	getUserHome = func() (string, error) { return emptyHome, nil }
+
 	t.Run("default targets global config", func(t *testing.T) {
 		tempDir := t.TempDir()
 		getWd = func() (string, error) { return tempDir, nil }
@@ -178,3 +186,80 @@ func TestConfigCmd(t *testing.T) {
 		}
 	})
 }
+
+// TestConfigDiscoversGlobalAgents mirrors TestInitDiscoversGlobalAgents: the
+// re-discovery path must resolve agent directories against the user home, not
+// against the user config directory.
+func TestConfigDiscoversGlobalAgents(t *testing.T) {
+	origGetWd := getWd
+	origGetUserConfig := getUserConfig
+	origGetUserHome := getUserHome
+	defer func() {
+		getWd = origGetWd
+		getUserConfig = origGetUserConfig
+		getUserHome = origGetUserHome
+	}()
+
+	tests := []struct {
+		name      string
+		globalDir string
+		want      string
+	}{
+		{
+			name:      "discovers Pi which is global only",
+			globalDir: filepath.Join(".pi", "agent"),
+			want:      ".pi/agent/skills",
+		},
+		{
+			name:      "discovers global Gemini CLI",
+			globalDir: ".gemini",
+			want:      ".gemini/skills",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			root := t.TempDir()
+			homeDir := filepath.Join(root, "home")
+			configDir := filepath.Join(root, "xdg_config")
+			cwd := filepath.Join(root, "project")
+
+			if err := os.MkdirAll(filepath.Join(homeDir, tt.globalDir), 0755); err != nil {
+				t.Fatalf("failed to seed agent dir: %v", err)
+			}
+			if err := os.MkdirAll(cwd, 0755); err != nil {
+				t.Fatalf("failed to seed cwd: %v", err)
+			}
+
+			cfgPath := filepath.Join(configDir, "skill-sync", "skill-sync.yaml")
+			if err := os.MkdirAll(filepath.Dir(cfgPath), 0755); err != nil {
+				t.Fatalf("failed to seed config dir: %v", err)
+			}
+			if err := os.WriteFile(cfgPath, []byte("targets:\n  - stale\n"), 0644); err != nil {
+				t.Fatalf("failed to seed config: %v", err)
+			}
+
+			getWd = func() (string, error) { return cwd, nil }
+			getUserConfig = func() (string, error) { return configDir, nil }
+			getUserHome = func() (string, error) { return homeDir, nil }
+
+			cmd := NewConfigCmd()
+			var out bytes.Buffer
+			cmd.SetOut(&out)
+			cmd.SetArgs([]string{})
+
+			if err := cmd.Execute(); err != nil {
+				t.Fatalf("unexpected error: %v", err)
+			}
+
+			content, err := os.ReadFile(cfgPath)
+			if err != nil {
+				t.Fatalf("failed to read updated config: %v", err)
+			}
+
+			if !strings.Contains(string(content), tt.want) {
+				t.Errorf("expected config to contain %q, got:\n%s", tt.want, string(content))
+			}
+		})
+	}
+}
diff --git a/internal/cli/init.go b/internal/cli/init.go
index 2a0a6f3..e7f3519 100644
--- a/internal/cli/init.go
+++ b/internal/cli/init.go
@@ -37,6 +37,7 @@ func NewInitCmd() *cobra.Command {
 var (
 	getWd                   = os.Getwd
 	getUserConfig           = os.UserConfigDir
+	getUserHome             = os.UserHomeDir
 	stdinReader   io.Reader = os.Stdin
 	isTTY                   = func() bool {
 		st, err := os.Stdin.Stat()
@@ -83,9 +84,11 @@ func runInit(cmd *cobra.Command, local, force bool) error {
 		}
 	}
 
+	// Agent directories live under the user home, not under the user config
+	// directory. These two lookups must stay separate.
 	d := discovery.New()
 	d.Getwd = getWd
-	d.UserHomeDir = func() (string, error) { return getUserConfig() }
+	d.UserHomeDir = getUserHome
 
 	targets, err := d.Scan()
 	if err != nil {
diff --git a/internal/cli/init_test.go b/internal/cli/init_test.go
index 6f2625d..2bb4c02 100644
--- a/internal/cli/init_test.go
+++ b/internal/cli/init_test.go
@@ -11,15 +11,23 @@ import (
 func TestInitCmd(t *testing.T) {
 	origGetWd := getWd
 	origGetUserConfig := getUserConfig
+	origGetUserHome := getUserHome
 	origIsTTY := isTTY
 	origStdin := stdinReader
 	defer func() {
 		getWd = origGetWd
 		getUserConfig = origGetUserConfig
+		getUserHome = origGetUserHome
 		isTTY = origIsTTY
 		stdinReader = origStdin
 	}()
 
+	// Pin the home seam to an empty directory so these cases never discover the
+	// developer's real agent directories. Global discovery has dedicated
+	// coverage in TestInitDiscoversGlobalAgents.
+	emptyHome := t.TempDir()
+	getUserHome = func() (string, error) { return emptyHome, nil }
+
 	t.Run("local init creates file in cwd with skills suffix", func(t *testing.T) {
 		tempDir := t.TempDir()
 		getWd = func() (string, error) { return tempDir, nil }
@@ -192,3 +200,83 @@ func TestInitCmd(t *testing.T) {
 		}
 	})
 }
+
+// TestInitDiscoversGlobalAgents pins the home/config seam separation. Agent
+// directories live under the user home, not under the user config directory, so
+// init must keep those two lookups independent. Pi is the canary: it has no
+// local directory, so a collapsed seam makes it undiscoverable.
+func TestInitDiscoversGlobalAgents(t *testing.T) {
+	origGetWd := getWd
+	origGetUserConfig := getUserConfig
+	origGetUserHome := getUserHome
+	origIsTTY := isTTY
+	defer func() {
+		getWd = origGetWd
+		getUserConfig = origGetUserConfig
+		getUserHome = origGetUserHome
+		isTTY = origIsTTY
+	}()
+
+	tests := []struct {
+		name      string
+		globalDir string
+		want      string
+	}{
+		{
+			name:      "discovers Pi which is global only",
+			globalDir: filepath.Join(".pi", "agent"),
+			want:      ".pi/agent/skills",
+		},
+		{
+			name:      "discovers global Claude Code",
+			globalDir: ".claude",
+			want:      ".claude/skills",
+		},
+		{
+			name:      "discovers global OpenCode under .config",
+			globalDir: filepath.Join(".config", "opencode"),
+			want:      ".config/opencode/skills",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			root := t.TempDir()
+			homeDir := filepath.Join(root, "home")
+			// The config directory is deliberately a sibling of home, never its
+			// parent, so a seam that confuses the two cannot accidentally pass.
+			configDir := filepath.Join(root, "xdg_config")
+			cwd := filepath.Join(root, "project")
+
+			if err := os.MkdirAll(filepath.Join(homeDir, tt.globalDir), 0755); err != nil {
+				t.Fatalf("failed to seed agent dir: %v", err)
+			}
+			if err := os.MkdirAll(cwd, 0755); err != nil {
+				t.Fatalf("failed to seed cwd: %v", err)
+			}
+
+			getWd = func() (string, error) { return cwd, nil }
+			getUserConfig = func() (string, error) { return configDir, nil }
+			getUserHome = func() (string, error) { return homeDir, nil }
+			isTTY = func() bool { return false }
+
+			cmd := NewInitCmd()
+			var out bytes.Buffer
+			cmd.SetOut(&out)
+			cmd.SetArgs([]string{})
+
+			if err := cmd.Execute(); err != nil {
+				t.Fatalf("unexpected error: %v", err)
+			}
+
+			content, err := os.ReadFile(filepath.Join(configDir, "skill-sync", "skill-sync.yaml"))
+			if err != nil {
+				t.Fatalf("failed to read generated config: %v", err)
+			}
+
+			if !strings.Contains(string(content), tt.want) {
+				t.Errorf("expected config to contain %q, got:\n%s", tt.want, string(content))
+			}
+		})
+	}
+}
diff --git a/odd/tasks/fix-global-agent-discovery.md b/odd/tasks/fix-global-agent-discovery.md
new file mode 100644
index 0000000..b7b7d77
--- /dev/null
+++ b/odd/tasks/fix-global-agent-discovery.md
@@ -0,0 +1,82 @@
+# Fix global agent discovery in `init` and `config`
+
+## Problem
+
+`internal/cli/init.go:88` and `internal/cli/config.go:65` inject the user *config*
+directory into the discovery *home* seam:
+
+```go
+d.UserHomeDir = func() (string, error) { return getUserConfig() }
+```
+
+`getUserConfig` is `os.UserConfigDir` (`~/.config` on Linux), so `Discovery.Scan()`
+resolves every global agent directory to `~/.config/.pi/agent`, `~/.config/.claude`,
+etc. None of those exist, so no global agent is ever discovered.
+
+Pi is fully invisible because its `AgentConfig.LocalDir` is `""`
+(`internal/agent/discovery/discovery.go:52`): it has only a global path.
+
+The TUI is unaffected — `internal/tui/program.go:71,86` call `discovery.New()`
+without overriding the seam.
+
+## Root cause
+
+One package-level variable (`getUserConfig`) serves two distinct responsibilities:
+locating `skill-sync.yaml` and locating the user home for agent discovery.
+
+## Fix
+
+Split the seam: keep `getUserConfig` for config location, add `getUserHome`
+(`os.UserHomeDir`) for discovery.
+
+## Tasks
+
+- [x] 1. RED: test that `init` discovers a global-only agent (Pi) when home and
+      config directories differ.
+- [x] 2. GREEN: add the `getUserHome` seam and wire it in `init.go`.
+- [x] 3. RED: equivalent test for `config`.
+- [x] 4. GREEN: wire `getUserHome` in `config.go`.
+- [x] 5. Make existing `init`/`config` tests hermetic by stubbing `getUserHome`,
+      so they cannot read the developer's real home directory.
+- [x] 6. Full suite + manual CLI verification against the real home.
+
+## Evidence
+
+**RED (task 1)** — `go test ./internal/cli/ -run TestInitDiscoversGlobalAgents`:
+all three cases emitted an empty `targets:` list.
+
+**RED (task 3)** — `go test ./internal/cli/ -run TestConfigDiscoversGlobalAgents`:
+both cases emitted `targets: []`.
+
+**Task 5 was not cosmetic.** After wiring the real home seam, the pre-existing
+case `TestInitCmd/no_agents_found_prints_'no_skills_configured'` failed because it
+started discovering the developer's actual `~/.claude`, `~/.gemini` and
+`~/.pi/agent`. Those tests had been passing only because the broken seam pointed
+them at a directory that never existed. Both suites now pin `getUserHome` to an
+empty temporary directory.
+
+**GREEN** — `go test ./...`: all 14 packages pass. `go vet ./...` clean,
+`gofmt -l internal/cli/` empty.
+
+**Manual** — `XDG_CONFIG_HOME=/tmp/pitest/cfg skill-sync init` against the real
+home now produces:
+
+```yaml
+targets:
+  - /home/eezzekl/.config/opencode/skills
+  - /home/eezzekl/.claude/skills
+  - /home/eezzekl/.gemini/skills
+  - /home/eezzekl/.copilot/skills
+  - /home/eezzekl/.pi/agent/skills
+```
+
+Previously this was an empty `targets:` list.
+
+## Notes
+
+`~/.pi/agent/skills` does not exist yet. `Discovery.Scan` matches on the agent
+root (`~/.pi/agent`) and `init` appends `/skills`; `internal/sync/engine.go:43-56`
+creates missing target directories, so the first `sync` materializes it.
+
+Pi project-local skills remain out of scope: `AgentConfig.LocalDir` for Pi is
+`""` by design.