diff --git a/.beads/issues.jsonl b/.beads/issues.jsonl
index ec8c7dc..4e29d19 100644
--- a/.beads/issues.jsonl
+++ b/.beads/issues.jsonl
@@ -1,2 +1,3 @@
+{"id":"py-code-mode-0c9","title":"Fix MCP install commands to consistently use --base flag","status":"closed","priority":1,"issue_type":"bug","created_at":"2026-01-02T13:10:43.012292-08:00","created_by":"actae0n","updated_at":"2026-01-02T13:11:47.455148-08:00","closed_at":"2026-01-02T13:11:47.455148-08:00","close_reason":"Fixed: README.md, getting-started.md, dependencies.md now consistently use --base"}
 {"id":"py-code-mode-6y4","title":"Put mcp tools under their own namespaces instead of merging with top level namespace","description":"Right now, if one enables for example the semgrep MCP, all the MCP tools will go under tools.* namespace; they will not be grouped like tools.semgrep.*; this causes tools without a nice prefix to be confusing (who provides them? what are they for?)","status":"closed","priority":2,"issue_type":"task","created_at":"2026-01-02T01:44:05.333773-08:00","created_by":"actae0n","updated_at":"2026-01-02T02:37:35.39444-08:00","closed_at":"2026-01-02T02:37:35.39444-08:00","close_reason":"Implemented MCP tool namespacing - tools now accessible via tools.namespace.tool_name pattern"}
 {"id":"py-code-mode-y1l","title":"Session API ergonomics: convenience constructors","description":"Improve Session API ergonomics with convenience constructors (from_base, subprocess, inprocess). Make storage param required. Re-export executor types at top level. PR #53.","status":"closed","priority":0,"issue_type":"task","created_at":"2026-01-02T13:04:00.716049-08:00","created_by":"actae0n","updated_at":"2026-01-02T13:04:14.004424-08:00","closed_at":"2026-01-02T13:04:14.004424-08:00","close_reason":"Closed"}
diff --git a/README.md b/README.md
index b68fabd..31aa414 100644
--- a/README.md
+++ b/README.md
@@ -82,7 +82,7 @@ See [Session API](./docs/session-api.md) and [Executors](./docs/executors.md) fo
 **Also ships as an MCP server for Claude Code:**
 
 ```bash
-claude mcp add py-code-mode -- uvx --from git+https://github.com/xpcmdshell/py-code-mode.git@v0.9.0 py-code-mode-mcp
+claude mcp add py-code-mode -- uvx --from git+https://github.com/xpcmdshell/py-code-mode.git@v0.9.0 py-code-mode-mcp --base ~/.code-mode
 ```
 
 ## Features
diff --git a/docs/dependencies.md b/docs/dependencies.md
index d56d8e3..7fba9e7 100644
--- a/docs/dependencies.md
+++ b/docs/dependencies.md
@@ -94,10 +94,10 @@ When using py-code-mode as an MCP server, dependency tools are available:
 
 ```bash
 # Start with runtime deps enabled (default)
-py-code-mode-mcp --storage ~/.code-mode
+py-code-mode-mcp --base ~/.code-mode
 
 # Start with runtime deps disabled
-py-code-mode-mcp --storage ~/.code-mode --no-runtime-deps
+py-code-mode-mcp --base ~/.code-mode --no-runtime-deps
 ```
 
 **Available MCP tools:**
diff --git a/docs/getting-started.md b/docs/getting-started.md
index cd075a6..016d878 100644
--- a/docs/getting-started.md
+++ b/docs/getting-started.md
@@ -17,7 +17,7 @@ uv add git+https://github.com/xpcmdshell/py-code-mode.git@v0.9.0
 ```bash
 claude mcp add -s user py-code-mode \
   -- uvx --from git+https://github.com/xpcmdshell/py-code-mode.git@v0.9.0 \
-  py-code-mode-mcp --storage ~/.code-mode
+  py-code-mode-mcp --base ~/.code-mode
 ```
 
 **Project-scoped installation** (only in the current project):
@@ -25,7 +25,7 @@ claude mcp add -s user py-code-mode \
 ```bash
 claude mcp add -s project py-code-mode \
   -- uvx --from git+https://github.com/xpcmdshell/py-code-mode.git@v0.9.0 \
-  py-code-mode-mcp --storage ./.code-mode
+  py-code-mode-mcp --base ./.code-mode
 ```
 
 > **Note:** Without `-s user` or `-s project`, `claude mcp add` defaults to project scope based on your current directory. If you install from `~` without a scope flag, the server only works in that directory.
@@ -36,7 +36,7 @@ claude mcp add -s project py-code-mode \
 claude mcp list
 ```
 
-The storage directory will contain `skills/` and `artifacts/` subdirectories.
+The base directory will contain `skills/`, `artifacts/`, and optionally `tools/` subdirectories.
 
 ## Your First Session