diff --git a/docs/5-data-diffing/mcp-server.md b/docs/5-data-diffing/mcp-server.md
index d92ad1c..57037b0 100644
--- a/docs/5-data-diffing/mcp-server.md
+++ b/docs/5-data-diffing/mcp-server.md
@@ -35,7 +35,7 @@ Recce compares your current branch's dbt models against a baseline from your mai
 
 ## Prerequisites
 
-Before starting the MCP server, generate both artifact sets.
+Before starting the MCP server, generate your development artifacts. Base artifacts are recommended for full diffing but not required.
 
 ### Generate development artifacts
 
@@ -61,8 +61,8 @@ git stash pop                            # restore changes
 
 This creates `target-base/manifest.json` and `target-base/catalog.json`. The MCP server compares these two artifact sets to produce diffs.
 
-!!! warning
-    The MCP server will not start if either `target/manifest.json` or `target-base/manifest.json` is missing.
+!!! note
+    If `target-base/` is missing, the MCP server starts in **single-environment mode** — all tools remain available, but diff results show no changes because both sides reference the same data. Generate base artifacts to enable real comparisons.
 
 ## Installation
 
@@ -207,27 +207,41 @@ When connected, the MCP server exposes these tools to your AI agent:
 | `schema_diff` | Detect schema changes (added, removed, or modified columns and type changes) |
 | `row_count_diff` | Compare row counts between branches |
 | `profile_diff` | Statistical profiling comparison (min, max, avg, nulls, and more) |
-| `value_diff` | Compare actual data values between branches |
-| `top_k_diff` | Compare top-K value distributions |
-| `histogram_diff` | Compare value distributions as histograms |
 | `query` | Run arbitrary SQL against your warehouse |
 | `query_diff` | Run the same SQL against both branches and compare results |
+| `list_checks` | List all validation checks in the current session with their status |
+| `run_check` | Run a specific validation check by ID |
+
+### Check types available through `run_check`
+
+These check types are accessible as preset checks configured in `recce.yml` or created in the Recce instance. Your AI agent runs them with the `run_check` tool:
+
+| Check type | Description |
+|------------|-------------|
+| `value_diff` | Compare actual data values row by row between branches |
+| `top_k_diff` | Compare top-K value distributions |
+| `histogram_diff` | Compare value distributions as histograms |
+
+See [Preset checks](../7-cicd/preset-checks.md) for how to configure these check types.
+
+!!! note
+    If base artifacts (`target-base/`) are not present, the server starts in **single-environment mode** — all tools remain available, but diff results show no changes. Generate base artifacts to enable real comparisons.
 
 ## Troubleshooting
 
 ### MCP server fails to start
 
-The most common cause is missing dbt artifacts. Check that both artifact directories exist:
+The most common cause is missing dbt artifacts. Check that your dbt artifacts exist:
 
 ```shell
-ls target/manifest.json target-base/manifest.json
+ls target/manifest.json
 ```
 
-If either file is missing, follow the [Prerequisites](#prerequisites) section above.
+If missing, run `dbt docs generate` in your current branch. See [Prerequisites](#prerequisites).
 
-### "No such file or directory: target-base/manifest.json"
+### Diff results show no changes
 
-You need to generate base artifacts. See [Prerequisites](#prerequisites).
+If the server starts but all diffs return empty results, you are likely in single-environment mode (missing base artifacts). Follow the [Generate base artifacts](#generate-base-artifacts) steps to enable real comparisons.
 
 ### Port already in use (SSE mode)