diff --git a/EvoScientist/EvoScientist.py b/EvoScientist/EvoScientist.py
index 9fd28f9..f52e8b8 100644
--- a/EvoScientist/EvoScientist.py
+++ b/EvoScientist/EvoScientist.py
@@ -207,14 +207,20 @@ def create_cli_agent(workspace_dir: str | None = None, checkpointer=None):
     Args:
         workspace_dir: Optional per-session workspace directory. If provided,
             creates a fresh backend rooted at this path. If None, uses the
-            module-level default backend (./workspace).
+            module-level default backend.
         checkpointer: Optional LangGraph checkpointer. If None, falls back
             to ``InMemorySaver`` (non-persistent).
     """
+    from . import paths as _paths
+
     if checkpointer is None:
         from langgraph.checkpoint.memory import InMemorySaver  # type: ignore[import-untyped]
         checkpointer = InMemorySaver()
 
+    # Read paths dynamically so runtime set_workspace_root() changes are picked up
+    _mem_dir = str(_paths.MEMORY_DIR)
+    _usr_skills_dir = str(_paths.USER_SKILLS_DIR)
+
     if workspace_dir:
         set_active_workspace(workspace_dir)
         ws_backend = CustomSandboxBackend(
@@ -223,12 +229,12 @@ def create_cli_agent(workspace_dir: str | None = None, checkpointer=None):
             timeout=300,
         )
         sk_backend = MergedReadOnlyBackend(
-            primary_dir=USER_SKILLS_DIR,
+            primary_dir=_usr_skills_dir,
             secondary_dir=SKILLS_DIR,
         )
         # Memory always uses SHARED directory (not per-session) for cross-session persistence
         mem_backend = FilesystemBackend(
-            root_dir=MEMORY_DIR,
+            root_dir=_mem_dir,
             virtual_mode=True,
         )
         be = CompositeBackend(
@@ -242,7 +248,7 @@ def create_cli_agent(workspace_dir: str | None = None, checkpointer=None):
         be = backend
 
     mw = [
-        create_memory_middleware(MEMORY_DIR, extraction_model=chat_model),
+        create_memory_middleware(_mem_dir, extraction_model=chat_model),
     ]
 
     # Re-load MCP tools from current config (picks up /mcp add changes)
diff --git a/EvoScientist/cli/agent.py b/EvoScientist/cli/agent.py
index 9029194..7362460 100644
--- a/EvoScientist/cli/agent.py
+++ b/EvoScientist/cli/agent.py
@@ -4,7 +4,7 @@ import os
 from datetime import datetime
 from pathlib import Path
 
-from ..paths import new_run_dir, RUNS_DIR
+from ..paths import new_run_dir
 
 
 def _shorten_path(path: str) -> str:
@@ -21,8 +21,11 @@ def _shorten_path(path: str) -> str:
         return path
 
 
-def _deduplicate_run_name(name: str, runs_dir: Path = RUNS_DIR) -> str:
+def _deduplicate_run_name(name: str, runs_dir: Path | None = None) -> str:
     """Return *name* if available, otherwise *name_1*, *name_2*, etc."""
+    if runs_dir is None:
+        from ..paths import RUNS_DIR
+        runs_dir = RUNS_DIR
     if not (runs_dir / name).exists():
         return name
     i = 1
@@ -40,7 +43,8 @@ def _create_session_workspace(name: str | None = None) -> str:
               if *name* is None.
     """
     if name:
-        session_id = _deduplicate_run_name(name)
+        from ..paths import RUNS_DIR
+        session_id = _deduplicate_run_name(name, RUNS_DIR)
     else:
         session_id = datetime.now().strftime("%Y%m%d_%H%M%S")
     workspace_dir = str(new_run_dir(session_id))
diff --git a/EvoScientist/cli/commands.py b/EvoScientist/cli/commands.py
index 9bca010..3c1d468 100644
--- a/EvoScientist/cli/commands.py
+++ b/EvoScientist/cli/commands.py
@@ -11,7 +11,7 @@ import typer  # type: ignore[import-untyped]
 from rich.table import Table
 
 from ..stream.display import console
-from ..paths import ensure_dirs
+from ..paths import ensure_dirs, set_workspace_root
 from ._app import app, config_app, mcp_app
 from .agent import _deduplicate_run_name, _create_session_workspace, _load_agent
 from .mcp_ui import (
@@ -361,16 +361,19 @@ def _main_callback(
     # --use-cwd is kept for backward compat but is now the default behavior
     if use_cwd:
         workspace_dir = os.getcwd()
+        set_workspace_root(workspace_dir)
         workspace_fixed = True
     elif workdir:
         workspace_dir = os.path.abspath(os.path.expanduser(workdir))
         os.makedirs(workspace_dir, exist_ok=True)
+        set_workspace_root(workspace_dir)
         workspace_fixed = True
     elif mode:
         # Explicit --mode overrides default_workdir
         effective_mode = mode
         workspace_root = config.default_workdir or os.getcwd()
         workspace_root = os.path.abspath(os.path.expanduser(workspace_root))
+        set_workspace_root(workspace_root)
         if effective_mode == "run":
             runs_dir = Path(workspace_root, "runs")
             session_id = _deduplicate_run_name(name, runs_dir) if name else datetime.now().strftime("%Y%m%d_%H%M%S")
@@ -383,6 +386,7 @@ def _main_callback(
     elif config.default_workdir:
         # Use configured default workdir with configured mode
         workspace_root = os.path.abspath(os.path.expanduser(config.default_workdir))
+        set_workspace_root(workspace_root)
         effective_mode = config.default_mode
         if effective_mode == "run":
             runs_dir = Path(workspace_root, "runs")
@@ -395,11 +399,13 @@ def _main_callback(
             workspace_fixed = True
     else:
         effective_mode = config.default_mode
+        workspace_root = os.getcwd()
+        set_workspace_root(workspace_root)
         if effective_mode == "run":
             workspace_dir = _create_session_workspace(name)
             workspace_fixed = False
         else:  # daemon mode (default) — use current directory
-            workspace_dir = os.getcwd()
+            workspace_dir = workspace_root
             workspace_fixed = True
 
     # Ensure memory and skills subdirs exist in workspace
diff --git a/EvoScientist/cli/interactive.py b/EvoScientist/cli/interactive.py
index e75e587..8544221 100644
--- a/EvoScientist/cli/interactive.py
+++ b/EvoScientist/cli/interactive.py
@@ -204,8 +204,8 @@ def cmd_interactive(
     import nest_asyncio
     nest_asyncio.apply()
 
-    from ..EvoScientist import MEMORY_DIR
-    memory_dir = MEMORY_DIR
+    from .. import paths
+    memory_dir = str(paths.MEMORY_DIR)
 
     history_file = str(os.path.expanduser("~/.EvoScientist_history"))
     session = PromptSession(
diff --git a/EvoScientist/config/onboard.py b/EvoScientist/config/onboard.py
index b6398b0..55b77bd 100644
--- a/EvoScientist/config/onboard.py
+++ b/EvoScientist/config/onboard.py
@@ -671,8 +671,12 @@ def _step_workspace(config: EvoScientistConfig) -> tuple[str, str]:
 
     # Custom workdir (optional)
     current_default = config.default_workdir or ""
+    if current_default:
+        prompt_text = f"Workspace directory (Enter to keep '{current_default}'):"
+    else:
+        prompt_text = f"Workspace directory (Enter to use ./{cwd_short}/):"
     workdir = questionary.text(
-        f"Workspace directory (Enter to use ./{cwd_short}/):",
+        prompt_text,
         default=current_default,
         style=WIZARD_STYLE,
         qmark=QMARK,
diff --git a/EvoScientist/config/settings.py b/EvoScientist/config/settings.py
index 397f6c4..7af786c 100644
--- a/EvoScientist/config/settings.py
+++ b/EvoScientist/config/settings.py
@@ -52,7 +52,7 @@ class EvoScientistConfig:
         provider: Default LLM provider ('anthropic', 'openai', 'google-genai', or 'nvidia').
         model: Default model name (short name or full ID).
         default_mode: Default workspace mode ('daemon' or 'run').
-        default_workdir: Default workspace directory (empty = use ./workspace).
+        default_workdir: Default workspace directory (empty = use current working directory).
         max_concurrent: Maximum concurrent sub-agents.
         max_iterations: Maximum delegation iterations.
         show_thinking: Whether to show thinking panels in CLI.
diff --git a/EvoScientist/paths.py b/EvoScientist/paths.py
index b5e3c4b..fa16f34 100644
--- a/EvoScientist/paths.py
+++ b/EvoScientist/paths.py
@@ -26,6 +26,21 @@ MEMORY_DIR = _env_path("EVOSCIENTIST_MEMORY_DIR") or (WORKSPACE_ROOT / "memory")
 USER_SKILLS_DIR = _env_path("EVOSCIENTIST_SKILLS_DIR") or (WORKSPACE_ROOT / "skills")
 
 
+def set_workspace_root(path: str | Path) -> None:
+    """Update workspace root and re-derive dependent directories.
+
+    Directories with an explicit environment-variable override keep their
+    env-var value; all others are re-derived from the new root.
+    Also resets ``_active_workspace`` to the new root as a safe default.
+    """
+    global WORKSPACE_ROOT, RUNS_DIR, MEMORY_DIR, USER_SKILLS_DIR, _active_workspace
+    WORKSPACE_ROOT = Path(path).resolve()
+    _active_workspace = WORKSPACE_ROOT
+    RUNS_DIR = _env_path("EVOSCIENTIST_RUNS_DIR") or (WORKSPACE_ROOT / "runs")
+    MEMORY_DIR = _env_path("EVOSCIENTIST_MEMORY_DIR") or (WORKSPACE_ROOT / "memory")
+    USER_SKILLS_DIR = _env_path("EVOSCIENTIST_SKILLS_DIR") or (WORKSPACE_ROOT / "skills")
+
+
 def ensure_dirs() -> None:
     """Create runtime subdirectories (memory, skills) if they do not exist.
 
diff --git a/EvoScientist/tools/skills_manager.py b/EvoScientist/tools/skills_manager.py
index c380c87..8f7ab43 100644
--- a/EvoScientist/tools/skills_manager.py
+++ b/EvoScientist/tools/skills_manager.py
@@ -1,7 +1,7 @@
 """Skill installation and management for EvoScientist.
 
 This module provides functions for installing, listing, and uninstalling user skills.
-Skills are installed to USER_SKILLS_DIR (./workspace/skills/).
+Skills are installed to USER_SKILLS_DIR (defaults to <workspace>/skills/).
 
 Supported installation sources:
 - Local directory paths
@@ -37,7 +37,7 @@ from pathlib import Path
 
 import yaml
 
-from ..paths import USER_SKILLS_DIR
+from .. import paths
 
 
 @dataclass
@@ -220,7 +220,7 @@ def install_skill(source: str, dest_dir: str | None = None) -> dict:
         - path: installed path (if successful)
         - error: error message (if failed)
     """
-    dest_dir = dest_dir or str(USER_SKILLS_DIR)
+    dest_dir = dest_dir or str(paths.USER_SKILLS_DIR)
     os.makedirs(dest_dir, exist_ok=True)
 
     if _is_github_url(source):
@@ -370,7 +370,7 @@ def list_skills(include_system: bool = False) -> list[SkillInfo]:
     skills: list[SkillInfo] = []
 
     # User skills
-    user_dir = Path(USER_SKILLS_DIR)
+    user_dir = Path(paths.USER_SKILLS_DIR)
     if user_dir.exists():
         for entry in sorted(user_dir.iterdir()):
             if entry.is_dir() and _validate_skill_dir(entry):
@@ -421,7 +421,7 @@ def uninstall_skill(name: str) -> dict:
         - success: bool
         - error: error message (if failed)
     """
-    user_dir = Path(USER_SKILLS_DIR).resolve()
+    user_dir = Path(paths.USER_SKILLS_DIR).resolve()
 
     # Validate name to prevent path traversal
     clean_name = _sanitize_name(name)
diff --git a/README.md b/README.md
index 22375c3..1a1108a 100644
--- a/README.md
+++ b/README.md
@@ -239,25 +239,27 @@ The channel can also be started manually with `/channel` in the interactive CLI.
 
 ### Runtime Directories
 
-By default, the **workspace** is created under the current directory:
+By default, the **workspace root** is the current working directory. Sub-directories
+are created automatically:
 
 ```
-./workspace/
+<cwd>/
   memory/   # shared MEMORY.md (persistent across sessions)
   skills/   # user-installed skills
-  runs/     # per-session workspaces
+  runs/     # per-session workspaces (run mode only)
 ```
 
-You can force workspace to be the current directory via `--use-cwd`.
+Use `--workdir` to set a different workspace root, or configure it via
+`EvoSci config set default_workdir /path/to/workspace`.
 
 Override individual paths via environment variables:
 
 | Variable | Default | Description |
 |----------|---------|-------------|
-| `EVOSCIENTIST_WORKSPACE_DIR` | `./workspace` | Root workspace directory |
-| `EVOSCIENTIST_RUNS_DIR` | `./workspace/runs` | Per-session run directories |
-| `EVOSCIENTIST_MEMORY_DIR` | `./workspace/memory` | Shared memory storage |
-| `EVOSCIENTIST_SKILLS_DIR` | `./workspace/skills` | User-installed skills |
+| `EVOSCIENTIST_WORKSPACE_DIR` | current directory | Root workspace directory |
+| `EVOSCIENTIST_RUNS_DIR` | `<workspace>/runs` | Per-session run directories |
+| `EVOSCIENTIST_MEMORY_DIR` | `<workspace>/memory` | Shared memory storage |
+| `EVOSCIENTIST_SKILLS_DIR` | `<workspace>/skills` | User-installed skills |
 
 ### Script Inference
 ```python
diff --git a/tests/test_paths.py b/tests/test_paths.py
new file mode 100644
index 0000000..d20929f
--- /dev/null
+++ b/tests/test_paths.py
@@ -0,0 +1,105 @@
+"""Tests for EvoScientist.paths — set_workspace_root and ensure_dirs."""
+
+import os
+from unittest import mock
+
+import pytest
+
+from EvoScientist import paths
+
+
+@pytest.fixture(autouse=True)
+def _restore_paths():
+    """Snapshot module-level path globals and restore after each test."""
+    orig = {
+        "WORKSPACE_ROOT": paths.WORKSPACE_ROOT,
+        "RUNS_DIR": paths.RUNS_DIR,
+        "MEMORY_DIR": paths.MEMORY_DIR,
+        "USER_SKILLS_DIR": paths.USER_SKILLS_DIR,
+        "_active_workspace": paths._active_workspace,
+    }
+    yield
+    paths.WORKSPACE_ROOT = orig["WORKSPACE_ROOT"]
+    paths.RUNS_DIR = orig["RUNS_DIR"]
+    paths.MEMORY_DIR = orig["MEMORY_DIR"]
+    paths.USER_SKILLS_DIR = orig["USER_SKILLS_DIR"]
+    paths._active_workspace = orig["_active_workspace"]
+
+
+class TestSetWorkspaceRoot:
+    """Tests for set_workspace_root()."""
+
+    def test_updates_derived_dirs(self, tmp_path):
+        """set_workspace_root should update WORKSPACE_ROOT and all derived dirs."""
+        new_root = tmp_path / "my_workspace"
+        new_root.mkdir()
+
+        paths.set_workspace_root(new_root)
+
+        assert paths.WORKSPACE_ROOT == new_root.resolve()
+        assert paths.RUNS_DIR == new_root.resolve() / "runs"
+        assert paths.MEMORY_DIR == new_root.resolve() / "memory"
+        assert paths.USER_SKILLS_DIR == new_root.resolve() / "skills"
+
+    def test_resets_active_workspace(self, tmp_path):
+        """set_workspace_root should reset _active_workspace to new root."""
+        new_root = tmp_path / "ws"
+        new_root.mkdir()
+
+        # Set active workspace to something different first
+        paths._active_workspace = tmp_path / "other"
+
+        paths.set_workspace_root(new_root)
+
+        assert paths._active_workspace == new_root.resolve()
+
+    def test_preserves_env_overrides(self, tmp_path):
+        """Dirs set via env vars should NOT be overwritten by set_workspace_root."""
+        custom_mem = tmp_path / "custom_memory"
+        custom_skills = tmp_path / "custom_skills"
+        custom_runs = tmp_path / "custom_runs"
+
+        env = {
+            "EVOSCIENTIST_MEMORY_DIR": str(custom_mem),
+            "EVOSCIENTIST_SKILLS_DIR": str(custom_skills),
+            "EVOSCIENTIST_RUNS_DIR": str(custom_runs),
+        }
+
+        new_root = tmp_path / "ws"
+        new_root.mkdir()
+
+        with mock.patch.dict(os.environ, env):
+            paths.set_workspace_root(new_root)
+
+            # WORKSPACE_ROOT and _active_workspace should still update
+            assert paths.WORKSPACE_ROOT == new_root.resolve()
+            assert paths._active_workspace == new_root.resolve()
+
+            # Derived dirs should reflect the env overrides, not the new root
+            assert paths.MEMORY_DIR == custom_mem.expanduser()
+            assert paths.USER_SKILLS_DIR == custom_skills.expanduser()
+            assert paths.RUNS_DIR == custom_runs.expanduser()
+
+    def test_accepts_string_path(self, tmp_path):
+        """set_workspace_root should accept str as well as Path."""
+        new_root = tmp_path / "str_ws"
+        new_root.mkdir()
+
+        paths.set_workspace_root(str(new_root))
+
+        assert paths.WORKSPACE_ROOT == new_root.resolve()
+
+
+class TestEnsureDirsUsesUpdatedPaths:
+    """ensure_dirs should create dirs at the currently set paths."""
+
+    def test_ensure_dirs_uses_updated_paths(self, tmp_path):
+        """After set_workspace_root, ensure_dirs creates dirs at new location."""
+        new_root = tmp_path / "workspace"
+        new_root.mkdir()
+
+        paths.set_workspace_root(new_root)
+        paths.ensure_dirs()
+
+        assert (new_root / "memory").is_dir()
+        assert (new_root / "skills").is_dir()
diff --git a/tests/test_skills_manager.py b/tests/test_skills_manager.py
index 266d5e2..bdf2a2d 100644
--- a/tests/test_skills_manager.py
+++ b/tests/test_skills_manager.py
@@ -272,7 +272,7 @@ class TestListSkills:
     """Tests for list_skills function."""
 
     def test_list_empty_dir(self, temp_skills_dir):
-        with patch("EvoScientist.tools.skills_manager.USER_SKILLS_DIR", temp_skills_dir):
+        with patch("EvoScientist.paths.USER_SKILLS_DIR", temp_skills_dir):
             skills = list_skills(include_system=False)
             assert skills == []
 
@@ -280,7 +280,7 @@ class TestListSkills:
         # Install a skill
         install_skill(str(sample_skill_dir), str(temp_skills_dir))
 
-        with patch("EvoScientist.tools.skills_manager.USER_SKILLS_DIR", temp_skills_dir):
+        with patch("EvoScientist.paths.USER_SKILLS_DIR", temp_skills_dir):
             skills = list_skills(include_system=False)
 
             assert len(skills) == 1
@@ -302,7 +302,7 @@ description: Skill number {i}
             )
             install_skill(str(skill_dir), str(temp_skills_dir))
 
-        with patch("EvoScientist.tools.skills_manager.USER_SKILLS_DIR", temp_skills_dir):
+        with patch("EvoScientist.paths.USER_SKILLS_DIR", temp_skills_dir):
             skills = list_skills(include_system=False)
 
             assert len(skills) == 3
@@ -324,7 +324,7 @@ class TestUninstallSkill:
         # Install first
         install_skill(str(sample_skill_dir), str(temp_skills_dir))
 
-        with patch("EvoScientist.tools.skills_manager.USER_SKILLS_DIR", temp_skills_dir):
+        with patch("EvoScientist.paths.USER_SKILLS_DIR", temp_skills_dir):
             result = uninstall_skill("sample-skill")
 
             assert result["success"] is True
@@ -334,7 +334,7 @@ class TestUninstallSkill:
             assert not skill_path.exists()
 
     def test_uninstall_nonexistent_skill(self, temp_skills_dir):
-        with patch("EvoScientist.tools.skills_manager.USER_SKILLS_DIR", temp_skills_dir):
+        with patch("EvoScientist.paths.USER_SKILLS_DIR", temp_skills_dir):
             result = uninstall_skill("nonexistent-skill")
 
             assert result["success"] is False