diff --git a/internal/agent/agent.go b/internal/agent/agent.go
index 119aa0c..4177e71 100644
--- a/internal/agent/agent.go
+++ b/internal/agent/agent.go
@@ -14,6 +14,10 @@ type Agent interface {
 	Name() string
 }
 
+// GlobalWorkDir is the target codebase directory for agent subprocesses.
+// Set this before running agents to ensure they operate on the correct codebase.
+var GlobalWorkDir string
+
 // shellQuote quotes a string for safe use in shell commands
 func shellQuote(s string) string {
 	// Use single quotes and escape any single quotes in the string
diff --git a/internal/agent/claude.go b/internal/agent/claude.go
index bdf5a36..454f94d 100644
--- a/internal/agent/claude.go
+++ b/internal/agent/claude.go
@@ -102,6 +102,9 @@ func (a *ClaudeAgent) Run(ctx context.Context, prompt string) (<-chan string, <-
 		claudeArgs += " -p " + shellQuote(prompt)
 
 		cmd := exec.CommandContext(ctx, "bash", "-lc", claudeArgs)
+		if GlobalWorkDir != "" {
+			cmd.Dir = GlobalWorkDir
+		}
 
 		stdout, err := cmd.StdoutPipe()
 		if err != nil {
diff --git a/internal/agent/codex.go b/internal/agent/codex.go
index 14f40f4..d879cbb 100644
--- a/internal/agent/codex.go
+++ b/internal/agent/codex.go
@@ -63,6 +63,9 @@ func (a *CodexAgent) Run(ctx context.Context, prompt string) (<-chan string, <-c
 		codexArgs += " -"
 
 		cmd := exec.CommandContext(ctx, "bash", "-lc", codexArgs)
+		if GlobalWorkDir != "" {
+			cmd.Dir = GlobalWorkDir
+		}
 		cmd.Stdin = strings.NewReader(prompt)
 
 		stdout, err := cmd.StdoutPipe()
diff --git a/internal/agent/gemini.go b/internal/agent/gemini.go
index 7ed780f..78659e3 100644
--- a/internal/agent/gemini.go
+++ b/internal/agent/gemini.go
@@ -56,6 +56,9 @@ func (a *GeminiAgent) Run(ctx context.Context, prompt string) (<-chan string, <-
 		}
 
 		cmd := exec.CommandContext(ctx, "bash", "-lc", geminiArgs)
+		if GlobalWorkDir != "" {
+			cmd.Dir = GlobalWorkDir
+		}
 		cmd.Stdin = strings.NewReader(prompt)
 
 		stdout, err := cmd.StdoutPipe()
diff --git a/internal/cli/assess.go b/internal/cli/assess.go
index c45c094..4f184fb 100644
--- a/internal/cli/assess.go
+++ b/internal/cli/assess.go
@@ -52,6 +52,11 @@ func runAssess(cmd *cobra.Command, args []string) error {
 		return fmt.Errorf("failed to load plan: %w", err)
 	}
 
+	// Set working directory for agent subprocesses from plan
+	if p.CodebaseRoot != "" {
+		agent.GlobalWorkDir = p.CodebaseRoot
+	}
+
 	display.PrintHeader("ASSESS")
 	display.PrintStatus("Plan: %s", p.Name)
 
diff --git a/internal/cli/complete.go b/internal/cli/complete.go
index 489f2c3..af62933 100644
--- a/internal/cli/complete.go
+++ b/internal/cli/complete.go
@@ -53,6 +53,11 @@ func runComplete(cmd *cobra.Command, args []string) error {
 		return fmt.Errorf("failed to load plan: %w", err)
 	}
 
+	// Set working directory for agent subprocesses from plan
+	if p.CodebaseRoot != "" {
+		agent.GlobalWorkDir = p.CodebaseRoot
+	}
+
 	display.PrintHeader("SYNTHESIZE")
 	display.PrintStatus("Plan: %s", p.Name)
 	display.PrintStatus("Subsystem: %s", completeSubsystem)
diff --git a/internal/cli/convene.go b/internal/cli/convene.go
index 04b0771..393270d 100644
--- a/internal/cli/convene.go
+++ b/internal/cli/convene.go
@@ -95,6 +95,11 @@ func runConvene(cmd *cobra.Command, args []string) error {
 		return fmt.Errorf("failed to load plan: %w", err)
 	}
 
+	// Set working directory for agent subprocesses from plan
+	if p.CodebaseRoot != "" {
+		agent.GlobalWorkDir = p.CodebaseRoot
+	}
+
 	display.PrintHeader("CONVENE")
 	display.PrintStatus("Plan: %s", p.Name)
 	display.PrintStatus("Subsystem: %s", conveneSubsystem)
diff --git a/internal/cli/plan.go b/internal/cli/plan.go
index 94be1c7..2e4206b 100644
--- a/internal/cli/plan.go
+++ b/internal/cli/plan.go
@@ -52,6 +52,9 @@ func runPlan(cmd *cobra.Command, args []string) error {
 		return fmt.Errorf("path must be a directory: %s", absPath)
 	}
 
+	// Set working directory for all agent subprocesses
+	agent.GlobalWorkDir = absPath
+
 	// Initialize state directory
 	st, err := state.New(absPath)
 	if err != nil {
diff --git a/internal/cli/run.go b/internal/cli/run.go
index 3e91bf9..b948950 100644
--- a/internal/cli/run.go
+++ b/internal/cli/run.go
@@ -83,6 +83,9 @@ func runFull(cmd *cobra.Command, args []string) error {
 		return fmt.Errorf("path must be a directory: %s", absPath)
 	}
 
+	// Set working directory for all agent subprocesses
+	agent.GlobalWorkDir = absPath
+
 	// Initialize state
 	st, err := state.New(absPath)
 	if err != nil {