Merge branch 'main' into docs-mcp-tool-count-15

MCP's stdio transport uses stdout for JSON-RPC framing, so anything else written there corrupts every response after it. The original #1134 bug was progress-tracker output landing on stdout during tool calls that construct a `ContextGraph`, which is exactly what happens on any request that triggers reasoning or extraction. This PR closes out the remaining pieces of that fix: loading now goes through `load_from_file()` instead of the older `load()` path on the root graph, and mutations, `record_decision`, `add_entity`, `add_relationship`, now persist back to `SEMANTICA_KG_PATH` when it's configured, in both MCP server implementations (the root `mcp/` package and the packaged `semantica.mcp_server`), not just one.

Four things came out of review on top of that.

The stdio regression test originally exercised `get_graph_summary`, which doesn't touch the progress tracker at all, so it couldn't have caught the original bug. Swapped it for `run_reasoning`: `Reasoner.infer_with_results()` calls `progress_tracker.start_tracking()` directly, the exact call site that corrupted stdout before, so this is the minimal path that actually proves the fix. The test now spawns a real `python -m mcp` subprocess, sends it a `tools/call` for `run_reasoning`, and asserts every single line on stdout parses as JSON.

Loading a corrupt or unreadable `SEMANTICA_KG_PATH` used to fail silently and fall through to an empty graph, which meant the next mutation would happily save that empty graph over the original file. Both implementations now track whether the initial load actually succeeded. If it didn't, every mutation handler refuses to save and returns an error instead, so a broken file on disk stays broken rather than getting silently replaced with nothing. An empty file is treated differently: that's a fresh destination, not a corrupt one, and starts a normal empty graph without tripping the guard.

`save_to_file` used to `open(path, 'w')` and `json.dump` directly into the destination, so a crash or disk-full error mid-write could leave a truncated file as the only copy of the graph. It now writes to a temp file in the same directory, flushes, fsyncs, and only then `os.replace`s the destination, so the destination is always either the old contents or the new contents, never a partial write. The temp file gets cleaned up if anything fails before the replace.

And since a mutation is applied to the in-memory graph before the save happens, a save failure used to leave the in-memory graph ahead of what's on disk, an entity or decision the client thinks succeeded but that never made it to the file. `record_decision`, `add_entity`, and `add_relationship` all roll back the in-memory mutation now if `save_to_file` raises, so the client-visible state and the persisted state never diverge: either both hold the change or neither does.

104 tests passing across the MCP, persistence, and progress-tracking suites.

docs/choose-your-module.md

@@ -226,7 +226,7 @@ Pick your goal to see the minimum imports and a working skeleton.
   </Tab>
 
   <Tab title="MCP — Claude / Cursor">
-    Use Semantica from Claude Desktop, Cursor, VS Code, or any MCP-aware tool — no Python code required after setup. 12 tools available instantly.
+    Use Semantica from Claude Desktop, Cursor, VS Code, or any MCP-aware tool — no Python code required after setup. 15 tools available instantly.
 
     **Step 1 — Install:**
     ```bash

docs/cli-setup.md

@@ -53,7 +53,7 @@ python -c "import semantica; print(semantica.__version__)"
 - **semantica-server** — Starts the REST API server. Binds to `0.0.0.0:8000`. Use this when another service or application needs programmatic access to Semantica over HTTP.
 - **semantica-worker** — Background task processor. Run alongside `semantica-server` when you need async pipeline execution outside the request cycle. Start the server first, then start one or more workers pointing at the same backend.
 - **semantica-explorer** — Launches the browser dashboard. Requires `pip install semantica[explorer]`. Use this to explore a saved knowledge graph interactively. See [Explorer Setup](explorer-setup).
-- **semantica-mcp** — Runs the MCP server over stdio. Configure it in your MCP client's settings file to expose all 12 tools and 3 resources to Claude Desktop, Cursor, Windsurf, or any MCP-aware client. See [MCP Server](reference/mcp_server).
+- **semantica-mcp** — Runs the MCP server over stdio. Configure it in your MCP client's settings file to expose all 15 tools and 3 resources to Claude Desktop, Cursor, Windsurf, or any MCP-aware client. See [MCP Server](reference/mcp_server).
 
 
 ## Usage Examples
@@ -229,6 +229,6 @@ Install the [Microsoft Visual C++ Redistributable](https://aka.ms/vs/17/release/
 ## Next Steps
 
 - [Explorer Setup](explorer-setup) — Build a graph, save it, and launch the browser dashboard.
-- [MCP Server](reference/mcp_server) — All 12 tools and 3 resources exposed over the MCP protocol.
+- [MCP Server](reference/mcp_server) — All 15 tools and 3 resources exposed over the MCP protocol.
 - [Installation](installation) — Virtual environments, optional extras, and platform-specific notes.
 - [Quickstart](quickstart) — End-to-end pipeline walkthrough with working code.

docs/getting-started.md

@@ -183,7 +183,7 @@ icon: "rocket"
     }
     ```
 
-    12 tools available instantly: extract entities, query graph, record decisions, run reasoning, export results.
+    15 tools available instantly: extract entities, query graph, record decisions, run reasoning, export results.
 
     **Next:** [MCP Server reference →](reference/mcp_server)
   </Tab>

docs/guides/mcp-server.md

@@ -11,7 +11,7 @@ MCP stands for the Model Context Protocol. It is an open standard that allows ex
 The Semantica MCP server exposes your knowledge graph as 12 callable tools. By connecting it, any compatible AI client can traverse the graph live, record decisions, run analytics, and export results during a conversation — without you having to write custom tool wrappers.
 
 <Info>
-  The Semantica MCP server exposes 12 tools and 3 read-only resources. All tools accept and return JSON. No configuration beyond an optional environment variable for graph persistence is required.
+  The Semantica MCP server exposes 15 tools and 3 read-only resources. All tools accept and return JSON. No configuration beyond an optional environment variable for graph persistence is required.
 </Info>
 
 ## Architecture & Communication
@@ -132,7 +132,7 @@ docker run --rm -i \
   ghcr.io/semantica-agi/semantica-mcp:latest
 ```
 
-## What the Agent Can Do: The 12 Tools
+## What the Agent Can Do: The 15 Tools
 
 Once connected, the LLM can call any of these tools during a conversation. The agent chains them automatically — you do not orchestrate the sequence, you just describe what you want.
 
@@ -140,6 +140,8 @@ Once connected, the LLM can call any of these tools during a conversation. The a
 
 **Knowledge graph manipulation** — `add_entity` adds a node, `add_relationship` adds a directed edge. After extraction, the agent calls these to persist what it found into the live graph.
 
+**Live graph queries and edits** — `query_graph` reads the graph without exporting it: fetch one node, walk its neighbours up to five hops, or keyword-search nodes. `update_node` merges properties onto an existing node (for example marking a task node `done`), and `delete_node` archives a node it no longer tracks. When `SEMANTICA_KG_PATH` is set, `update_node` and `delete_node` write their changes back to that file so they survive a restart.
+
 **Decision intelligence** — `record_decision` writes a decision as a provenance node with confidence score, reasoning, and decision maker identity. `query_decisions` retrieves past decisions by query or category. `find_precedents` finds the most similar past decisions by semantic similarity. `get_causal_chain` traces decision causality upstream or downstream.
 
 **Reasoning** — `run_reasoning` applies forward-chaining IF/THEN rules over a set of facts and returns derived conclusions.

docs/index.md

@@ -369,7 +369,7 @@ Semantica was designed for domains where every decision must be explainable and
 | `semantica.reasoning` | Forward chaining, Rete, deductive, abductive, SPARQL, Datalog |
 | `semantica.ontology` | SHACL, SKOS, alignments, diff/migration, auto-generation, OWL/RDF |
 | `semantica.explorer` | FastAPI Knowledge Explorer, Ontology Hub, Distance Intelligence, SHACL Studio |
-| `semantica.mcp_server` | MCP stdio server: 12 tools for Claude Desktop, VS Code, Cursor, Windsurf, Cline |
+| `semantica.mcp_server` | MCP stdio server: 15 tools for Claude Desktop, VS Code, Cursor, Windsurf, Cline |
 | `semantica.vector_store` | FAISS, Pinecone, Weaviate, Qdrant, Milvus, PgVector |
 | `semantica.graph_store` | Neo4j, FalkorDB, Apache AGE, Amazon Neptune |
 | `semantica.triplet_store` | In-memory and persistent RDF triple store with SPARQL |

docs/modules.md

@@ -438,7 +438,7 @@ Exposes Semantica as an MCP stdio server for IDE and agent integrations.
 python -m semantica.mcp_server
 ```
 
-**Integrations:** Claude Desktop, VS Code, Cursor, Windsurf, Cline: 12 MCP tools exposed
+**Integrations:** Claude Desktop, VS Code, Cursor, Windsurf, Cline: 15 MCP tools exposed
 
 ### Seed
 

docs/reference/mcp_server.md

@@ -6,7 +6,7 @@ icon: "plug"
 
 **`semantica.mcp_server`** exposes Semantica's knowledge graph, decision intelligence, semantic extraction, and reasoning capabilities as an [MCP (Model Context Protocol)](https://modelcontextprotocol.io) **server over stdio**:
 
-- 12 MCP tools exposed: extract entities, query graph, record decisions, run reasoning, export results
+- 15 MCP tools exposed: extract entities, query graph, record decisions, run reasoning, export results
 - No Python code required after launch: configure once, use from any MCP-aware client
 - Compatible with Claude Desktop, Windsurf, Cline, Continue, VS Code, Roo Code, Cursor
 
@@ -40,7 +40,7 @@ python -m semantica.mcp_server
 
 ## What You Get
 
-- **12 MCP Tools** — Extract entities, extract relations, record decisions, query decisions, find precedents, trace causal chains, add entities, add relationships, run analytics, summarise graph, run reasoning, export graph.
+- **15 MCP Tools** — Extract entities, extract relations, record decisions, query decisions, find precedents, trace causal chains, add entities, add relationships, run analytics, summarise graph, run reasoning, export graph, query the live graph, update nodes, archive nodes.
 - **3 Readable Resources** — Live graph JSON (`semantica://graph/summary`), decision list, and schema/version info: readable by any MCP client.
 - **Zero Infrastructure** — Runs over stdio: no server, no port, no Docker required. One config block to activate in any MCP client.
 - **Persistent Graphs** — Point `SEMANTICA_KG_PATH` at a saved graph file to reload it automatically on every server startup.
@@ -159,7 +159,7 @@ The MCP server is included in the base install: no extras required.
 
 ## Tools
 
-The MCP server exposes 12 tools that any connected AI assistant can call:
+The MCP server exposes 15 tools that any connected AI assistant can call:
 
 | Tool | Category | Description |
 | :---- | :-------- | :----------- |
@@ -173,6 +173,9 @@ The MCP server exposes 12 tools that any connected AI assistant can call:
 | `add_relationship` | Graph Operations | Add a directed edge between two nodes |
 | `get_graph_summary` | Graph Operations | Node count, decision count, graph status |
 | `get_graph_analytics` | Graph Operations | PageRank centrality and community detection |
+| `query_graph` | Graph Operations | Fetch a node, traverse its neighbours, or keyword-search nodes |
+| `update_node` | Graph Operations | Merge properties onto a node and persist to `SEMANTICA_KG_PATH` |
+| `delete_node` | Graph Operations | Soft-delete (archive) a node and persist to `SEMANTICA_KG_PATH` |
 | `run_reasoning` | Reasoning | Forward-chain IF/THEN rules over facts |
 | `export_graph` | Reasoning & Export | Serialise the graph (`turtle`/`ttl`: RDF Turtle aliases, `nt`, `xml`, `json-ld`, `json`) |
 
@@ -386,6 +389,51 @@ Takes no input parameters.
 
 </Accordion>
 
+<Accordion title="query_graph" icon="magnifying-glass">
+
+Read the live graph in one of three modes, set by `mode`:
+
+- `node` — return a single node by `node_id`.
+- `neighbors` (default) — traverse outward and inward from `node_id` up to `depth` hops (clamped to 1-5, default 1). Optional `relationship_types` filters edge types; optional `limit` caps results.
+- `search` — keyword match `query` against each node's id and content. Optional `node_type` restricts the scan; `limit` defaults to 50.
+
+**Input:**
+
+```json
+{ "mode": "neighbors", "node_id": "apple_inc", "depth": 2 }
+```
+
+</Accordion>
+
+<Accordion title="update_node" icon="pen">
+
+Merge a set of properties onto an existing node. The change is applied in memory and, when `SEMANTICA_KG_PATH` is set, written back to that file so it survives a restart. Returns `persisted: false` when no path is configured.
+
+**Input:**
+
+```json
+{
+  "node_id": "task_42",
+  "properties": { "status": "done", "note": "shipped in v0.6.7" }
+}
+```
+
+`node_id` and a non-empty `properties` object are required. Updating a missing node returns an error.
+
+</Accordion>
+
+<Accordion title="delete_node" icon="box-archive">
+
+Soft-delete a node: it stays in the graph for history but is marked `status: "archived"`. Persists to `SEMANTICA_KG_PATH` when configured.
+
+**Input:**
+
+```json
+{ "node_id": "task_42" }
+```
+
+</Accordion>
+
 </AccordionGroup>
 
 ### Reasoning

mcp/README.md

@@ -8,8 +8,9 @@ Connects Claude Code, Cursor, Windsurf, Cline, Continue, VS Code (GitHub Copilot
 ## Quick start
 
 ```bash
-# From the repo root
-pip install -e ".[mcp]"
+# From the repo root — no extra install flag needed; the root mcp/ package is
+# part of the repository and does not require an external MCP SDK.
+pip install -e .
 
 # Test the server (type a JSON-RPC request, press Enter)
 python -m mcp
@@ -89,7 +90,14 @@ python -m mcp [--debug]
 
 ## Per-tool configuration
 
-### Claude Code (`~/.claude/settings.json`)
+### Claude Code (`~/.claude.json` or `.mcp.json`)
+
+Claude Code supports two MCP configuration scopes:
+
+- **User scope** — `~/.claude.json` applies across all projects for your user account.
+- **Project scope** — `.mcp.json` in your project root applies only to that project.
+
+Both files use the same `mcpServers` structure:
 
 ```json
 {
@@ -97,15 +105,33 @@ python -m mcp [--debug]
     "semantica": {
       "command": "python",
       "args": ["-m", "mcp"],
-      "cwd": "/path/to/semantica"
+      "env": {
+        "PYTHONPATH": "/path/to/semantica"
+      }
     }
   }
 }
 ```
 
-Or use the plugin bundle:
+> **Why `PYTHONPATH`?**  The root `mcp/` package is intentionally not included in
+> the installed wheel, so `python -m mcp` only works when the repository is on
+> Python's import path.  Setting `PYTHONPATH` here ensures this works regardless
+> of the working directory Claude uses when it launches the server.
+
+Or add it via the CLI (user scope):
+
 ```bash
-claude mcp add semantica python -m mcp --cwd /path/to/semantica
+claude mcp add --scope user semantica \
+  -e PYTHONPATH=/path/to/semantica \
+  -- python -m mcp
+```
+
+Or for project scope (omit `--scope user`):
+
+```bash
+claude mcp add semantica \
+  -e PYTHONPATH=/path/to/semantica \
+  -- python -m mcp
 ```
 
 ---
@@ -216,7 +242,7 @@ Add to your Q Developer MCP config:
 
 | Variable | Default | Description |
 |---|---|---|
-| `SEMANTICA_KG_PATH` | *(in-memory)* | Path to persist/load the graph (JSON file) |
+| `SEMANTICA_KG_PATH` | *(in-memory only)* | Path to a JSON file used to **load** the graph on startup and **persist** mutations (record decisions, add entities/relationships) back to disk after each change. When unset the graph lives in memory only and is lost when the server exits. |
 
 ---
 

mcp/session.py

@@ -16,6 +16,13 @@ log = logging.getLogger("semantica.mcp.session")
 
 _graph: Optional[Any] = None
 
+# Tracks whether the last graph initialisation successfully loaded the
+# configured SEMANTICA_KG_PATH file.  When True (or no path was configured)
+# mutation handlers are allowed to save.  When False an existing file failed
+# to load; saving would overwrite the original data with an empty graph, so
+# persistence is blocked until the process is restarted with a readable file.
+_load_ok: bool = True
+
 
 def get_graph() -> Any:
     """
@@ -24,24 +31,45 @@ def get_graph() -> Any:
     The graph is created with advanced_analytics=True so all centrality,
     community-detection, and embedding features are available.
     """
-    global _graph
+    global _graph, _load_ok
     if _graph is None:
         from semantica.context import ContextGraph
 
         _graph = ContextGraph(advanced_analytics=True)
+        _load_ok = True  # default: safe to persist
 
         kg_path = os.environ.get("SEMANTICA_KG_PATH", "").strip()
         if kg_path and os.path.exists(kg_path):
-            try:
-                _graph.load(kg_path)
-                log.info("Graph loaded from %s", kg_path)
-            except Exception as exc:
-                log.warning("Could not load graph from %s: %s", kg_path, exc)
+            # Only attempt to load if the file has content.  An empty file
+            # means the path was just created (e.g. a fresh tempfile) and
+            # should be treated as "start with empty graph" rather than a
+            # corrupt-file failure.
+            if os.path.getsize(kg_path) > 0:
+                try:
+                    _graph.load_from_file(kg_path)
+                    log.info("Graph loaded from %s", kg_path)
+                except Exception as exc:
+                    log.warning(
+                        "Could not load graph from %s: %s — persistence disabled "
+                        "to protect existing data; restart the server to retry.",
+                        kg_path, exc,
+                    )
+                    _load_ok = False  # do not overwrite the original file
 
     return _graph
 
 
+def is_persistence_safe() -> bool:
+    """Return True when it is safe to write mutations back to SEMANTICA_KG_PATH.
+
+    Returns False after a failed load so that mutation handlers do not
+    overwrite the original (possibly intact) file with a fresh empty graph.
+    """
+    return _load_ok
+
+
 def reset_graph() -> None:
     """Reset the singleton (mainly useful in tests)."""
-    global _graph
+    global _graph, _load_ok
     _graph = None
+    _load_ok = True

mcp/tools/decisions.py

@@ -5,6 +5,7 @@ Decision intelligence tools — record, query, precedents, causal chain, impact.
 from __future__ import annotations
 
 import logging
+import os
 
 from mcp.schemas import (
     ANALYZE_DECISION_IMPACT,
@@ -13,7 +14,7 @@ from mcp.schemas import (
     QUERY_DECISIONS,
     RECORD_DECISION,
 )
-from mcp.session import get_graph
+from mcp.session import get_graph, is_persistence_safe
 
 log = logging.getLogger("semantica.mcp.tools.decisions")
 
@@ -37,6 +38,39 @@ def handle_record_decision(args: dict) -> dict:
             valid_from=args.get("valid_from"),
             valid_until=args.get("valid_until"),
         )
+        # Persist back to disk so the decision survives server restarts.
+        # Skip when the initial load failed to avoid overwriting original data.
+        kg_path = os.environ.get("SEMANTICA_KG_PATH", "").strip()
+        if kg_path:
+            if not is_persistence_safe():
+                # Roll back the in-memory mutation so the client-visible state
+                # matches the persisted state (neither is saved).
+                if hasattr(graph, "_decisions") and decision_id in graph._decisions:
+                    del graph._decisions[decision_id]
+                    if hasattr(graph, "_decision_index"):
+                        cat = args.get("category", "")
+                        if cat in graph._decision_index:
+                            graph._decision_index[cat].discard(decision_id)
+                return {
+                    "error": (
+                        "Persistence blocked: the configured SEMANTICA_KG_PATH "
+                        "could not be loaded at startup. Restart the server with "
+                        "a readable graph file to re-enable persistence."
+                    )
+                }
+            try:
+                graph.save_to_file(kg_path)
+            except Exception as save_exc:
+                # Atomic write failed. Roll back the in-memory mutation so the
+                # client-visible and persisted states remain consistent.
+                if hasattr(graph, "_decisions") and decision_id in graph._decisions:
+                    del graph._decisions[decision_id]
+                    if hasattr(graph, "_decision_index"):
+                        cat = args.get("category", "")
+                        if cat in graph._decision_index:
+                            graph._decision_index[cat].discard(decision_id)
+                log.exception("save_to_file failed after record_decision; mutation rolled back")
+                return {"error": f"Mutation rolled back: could not persist graph: {save_exc}"}
         return {
             "decision_id": decision_id,
             "status": "recorded",

mcp/tools/graph.py

@@ -5,9 +5,10 @@ Graph tools — add entities/relationships, search, analytics, summary.
 from __future__ import annotations
 
 import logging
+import os
 
 from mcp.schemas import ADD_ENTITY, ADD_RELATIONSHIP, EMPTY, GET_ANALYTICS, SEARCH_GRAPH
-from mcp.session import get_graph
+from mcp.session import get_graph, is_persistence_safe
 
 log = logging.getLogger("semantica.mcp.tools.graph")
 
@@ -25,6 +26,35 @@ def handle_add_entity(args: dict) -> dict:
             node_type=args.get("type", "Entity"),
             metadata=args.get("metadata", {}),
         )
+        # Persist back to disk so the entity survives server restarts.
+        # Skip when the initial load failed to avoid overwriting original data.
+        kg_path = os.environ.get("SEMANTICA_KG_PATH", "").strip()
+        if kg_path:
+            if not is_persistence_safe():
+                # Roll back: remove the node we just added.
+                try:
+                    with graph._lock:
+                        graph._drop_node_from_indexes(node_id)
+                except Exception:
+                    pass
+                return {
+                    "error": (
+                        "Persistence blocked: the configured SEMANTICA_KG_PATH "
+                        "could not be loaded at startup. Restart the server with "
+                        "a readable graph file to re-enable persistence."
+                    )
+                }
+            try:
+                graph.save_to_file(kg_path)
+            except Exception as save_exc:
+                # Roll back: remove the node so in-memory and persisted state agree.
+                try:
+                    with graph._lock:
+                        graph._drop_node_from_indexes(node_id)
+                except Exception:
+                    pass
+                log.exception("save_to_file failed after add_entity; mutation rolled back")
+                return {"error": f"Mutation rolled back: could not persist graph: {save_exc}"}
         return {"status": "added", "id": node_id, "type": args.get("type", "Entity")}
     except Exception as exc:
         log.exception("add_entity failed")
@@ -46,6 +76,45 @@ def handle_add_relationship(args: dict) -> dict:
             edge_type=rel_type,
             metadata=args.get("metadata", {}),
         )
+        # Persist back to disk so the relationship survives server restarts.
+        # Skip when the initial load failed to avoid overwriting original data.
+        kg_path = os.environ.get("SEMANTICA_KG_PATH", "").strip()
+        if kg_path:
+            if not is_persistence_safe():
+                # Roll back: remove the edge we just added (last matching edge).
+                try:
+                    with graph._lock:
+                        for edge in reversed(list(graph.edges)):
+                            if (edge.source_id == source
+                                    and edge.target_id == target
+                                    and edge.edge_type == rel_type):
+                                graph._drop_edge_from_indexes(edge)
+                                break
+                except Exception:
+                    pass
+                return {
+                    "error": (
+                        "Persistence blocked: the configured SEMANTICA_KG_PATH "
+                        "could not be loaded at startup. Restart the server with "
+                        "a readable graph file to re-enable persistence."
+                    )
+                }
+            try:
+                graph.save_to_file(kg_path)
+            except Exception as save_exc:
+                # Roll back: remove the edge so in-memory and persisted state agree.
+                try:
+                    with graph._lock:
+                        for edge in reversed(list(graph.edges)):
+                            if (edge.source_id == source
+                                    and edge.target_id == target
+                                    and edge.edge_type == rel_type):
+                                graph._drop_edge_from_indexes(edge)
+                                break
+                except Exception:
+                    pass
+                log.exception("save_to_file failed after add_relationship; mutation rolled back")
+                return {"error": f"Mutation rolled back: could not persist graph: {save_exc}"}
         return {"status": "added", "source": source, "target": target, "type": rel_type}
     except Exception as exc:
         log.exception("add_relationship failed")

semantica/context/context_graph.py

@@ -1203,8 +1203,30 @@ class ContextGraph:
                 "links": links_data,
             }
 
-        with open(path, "w", encoding="utf-8") as f:
-            json.dump(data, f, indent=2, ensure_ascii=False)
+        # Write atomically: serialize to a sibling temp file then replace the
+        # destination in one OS-level rename.  This guarantees the destination
+        # is either the old contents or the new contents — never a partial write
+        # — so a crash or disk-full error during json.dump cannot corrupt the
+        # sole persisted copy of the graph.
+        dest = Path(path)
+        dest.parent.mkdir(parents=True, exist_ok=True)
+        fd, tmp_path = tempfile.mkstemp(
+            dir=dest.parent, prefix=".kg_tmp_", suffix=".json"
+        )
+        try:
+            with os.fdopen(fd, "w", encoding="utf-8") as f:
+                json.dump(data, f, indent=2, ensure_ascii=False)
+                f.flush()
+                os.fsync(f.fileno())
+            os.replace(tmp_path, dest)
+        except Exception:
+            # Clean up the temp file on any failure so we don't litter the
+            # directory with partial writes.
+            try:
+                os.unlink(tmp_path)
+            except OSError:
+                pass
+            raise
 
         self.logger.info(f"Saved context graph to {path}")
 

semantica/mcp_server/__init__.py

@@ -72,19 +72,34 @@ os.environ["SEMANTICA_DISABLE_PROGRESS"] = "1"
 # ── lazy graph session ──────────────────────────────────────────────────────
 _graph: Any = None
 
+# Tracks whether the last _get_graph() call successfully loaded the configured
+# SEMANTICA_KG_PATH file.  When False (load failed) mutation handlers skip
+# save_to_file to avoid overwriting the original file with an empty graph.
+_kg_load_ok: bool = True
+
 
 def _get_graph():
-    global _graph
+    global _graph, _kg_load_ok
     if _graph is None:
         from semantica.context import ContextGraph
         _graph = ContextGraph(advanced_analytics=True)
+        _kg_load_ok = True  # default: safe to persist
         kg_path = os.environ.get("SEMANTICA_KG_PATH")
         if kg_path and os.path.exists(kg_path):
-            try:
-                _graph.load_from_file(kg_path)
-                log.info("Loaded graph from %s", kg_path)
-            except Exception as exc:
-                log.warning("Could not load graph from %s: %s", kg_path, exc)
+            # Only attempt to load if the file has content.  An empty file
+            # means the path was just created (fresh destination) and should
+            # be treated as "start with empty graph" not a corrupt-file failure.
+            if os.path.getsize(kg_path) > 0:
+                try:
+                    _graph.load_from_file(kg_path)
+                    log.info("Loaded graph from %s", kg_path)
+                except Exception as exc:
+                    log.warning(
+                        "Could not load graph from %s: %s — persistence disabled "
+                        "to protect existing data; restart the server to retry.",
+                        kg_path, exc,
+                    )
+                    _kg_load_ok = False  # do not overwrite the original file
     return _graph
 
 
@@ -179,6 +194,35 @@ def _tool_record_decision(args: dict) -> dict:
         valid_from=args.get("valid_from"),
         valid_until=args.get("valid_until"),
     )
+    # Persist back to disk so the decision survives server restarts.
+    kg_path = os.environ.get("SEMANTICA_KG_PATH")
+    if kg_path:
+        if not _kg_load_ok:
+            # Roll back to keep in-memory state consistent with persisted state.
+            if hasattr(graph, "_decisions") and decision_id in graph._decisions:
+                del graph._decisions[decision_id]
+                if hasattr(graph, "_decision_index"):
+                    cat = args.get("category", "")
+                    if cat in graph._decision_index:
+                        graph._decision_index[cat].discard(decision_id)
+            return {
+                "error": (
+                    "Persistence blocked: the configured SEMANTICA_KG_PATH "
+                    "could not be loaded at startup. Restart the server to retry."
+                )
+            }
+        try:
+            graph.save_to_file(kg_path)
+        except Exception as save_exc:
+            # Atomic write failed. Roll back to keep states consistent.
+            if hasattr(graph, "_decisions") and decision_id in graph._decisions:
+                del graph._decisions[decision_id]
+                if hasattr(graph, "_decision_index"):
+                    cat = args.get("category", "")
+                    if cat in graph._decision_index:
+                        graph._decision_index[cat].discard(decision_id)
+            log.exception("save_to_file failed after record_decision; mutation rolled back")
+            return {"error": f"Mutation rolled back: could not persist graph: {save_exc}"}
     return {"decision_id": decision_id, "status": "recorded"}
 
 
@@ -246,6 +290,31 @@ def _tool_add_entity(args: dict) -> dict:
     graph = _get_graph()
     graph.add_node(node_id=node_id, label=label, node_type=node_type,
                    metadata=args.get("metadata", {}))
+    # Persist back to disk so the entity survives server restarts.
+    kg_path = os.environ.get("SEMANTICA_KG_PATH")
+    if kg_path:
+        if not _kg_load_ok:
+            try:
+                with graph._lock:
+                    graph._drop_node_from_indexes(node_id)
+            except Exception:
+                pass
+            return {
+                "error": (
+                    "Persistence blocked: the configured SEMANTICA_KG_PATH "
+                    "could not be loaded at startup. Restart the server to retry."
+                )
+            }
+        try:
+            graph.save_to_file(kg_path)
+        except Exception as save_exc:
+            try:
+                with graph._lock:
+                    graph._drop_node_from_indexes(node_id)
+            except Exception:
+                pass
+            log.exception("save_to_file failed after add_entity; mutation rolled back")
+            return {"error": f"Mutation rolled back: could not persist graph: {save_exc}"}
     return {"status": "added", "id": node_id}
 
 
@@ -259,6 +328,41 @@ def _tool_add_relationship(args: dict) -> dict:
     graph = _get_graph()
     graph.add_edge(source_id=source, target_id=target, edge_type=rel_type,
                    metadata=args.get("metadata", {}))
+    # Persist back to disk so the relationship survives server restarts.
+    kg_path = os.environ.get("SEMANTICA_KG_PATH")
+    if kg_path:
+        if not _kg_load_ok:
+            try:
+                with graph._lock:
+                    for edge in reversed(list(graph.edges)):
+                        if (edge.source_id == source
+                                and edge.target_id == target
+                                and edge.edge_type == rel_type):
+                            graph._drop_edge_from_indexes(edge)
+                            break
+            except Exception:
+                pass
+            return {
+                "error": (
+                    "Persistence blocked: the configured SEMANTICA_KG_PATH "
+                    "could not be loaded at startup. Restart the server to retry."
+                )
+            }
+        try:
+            graph.save_to_file(kg_path)
+        except Exception as save_exc:
+            try:
+                with graph._lock:
+                    for edge in reversed(list(graph.edges)):
+                        if (edge.source_id == source
+                                and edge.target_id == target
+                                and edge.edge_type == rel_type):
+                            graph._drop_edge_from_indexes(edge)
+                            break
+            except Exception:
+                pass
+            log.exception("save_to_file failed after add_relationship; mutation rolled back")
+            return {"error": f"Mutation rolled back: could not persist graph: {save_exc}"}
     return {"status": "added", "source": source, "target": target, "type": rel_type}
 
 

tests/context/test_decision_persistence_pr967.py

@@ -1037,5 +1037,195 @@ class TestClearResetsDecisionIndexes(unittest.TestCase):
         self.assertEqual(g._decisions[did]["category"], "new")
 
 
+# ---------------------------------------------------------------------------
+# Part 15: semantica.mcp_server mutation persistence (#1134)
+# ---------------------------------------------------------------------------
+
+class TestMCPServerMutationPersistence(unittest.TestCase):
+    """_tool_record_decision, _tool_add_entity, and _tool_add_relationship must
+    each call save_to_file when SEMANTICA_KG_PATH is configured so mutations
+    survive server restarts.
+
+    Mirrors update_node / delete_node which already had this behaviour from
+    PR #967.  These tests extend coverage to the three previously missing tools.
+    """
+
+    # ---- helpers --------------------------------------------------------
+
+    def _isolated_mcp_graph(self):
+        """Return a fresh ContextGraph injected as the mcp_server singleton."""
+        import semantica.mcp_server as mcp_mod
+        g = ContextGraph(advanced_analytics=False)
+        self._original_graph = mcp_mod._graph
+        mcp_mod._graph = g
+        return g
+
+    def _restore_mcp_graph(self):
+        import semantica.mcp_server as mcp_mod
+        mcp_mod._graph = self._original_graph
+
+    # ---- record_decision ------------------------------------------------
+
+    def test_record_decision_persists_to_kg_path(self):
+        """_tool_record_decision must write the graph to SEMANTICA_KG_PATH."""
+        from semantica.mcp_server import _tool_record_decision
+
+        g = self._isolated_mcp_graph()
+        try:
+            with tempfile.NamedTemporaryFile(suffix=".json", delete=False) as f:
+                path = f.name
+            try:
+                with patch.dict(os.environ, {"SEMANTICA_KG_PATH": path}):
+                    result = _tool_record_decision({
+                        "category": "mcp_server_persist",
+                        "scenario": "Testing packaged server persistence",
+                        "reasoning": "save_to_file must be called on mutation",
+                        "outcome": "verified",
+                        "confidence": 0.99,
+                    })
+
+                self.assertNotIn("error", result, result)
+                self.assertIn("decision_id", result)
+
+                # File must have been written.
+                self.assertGreater(os.path.getsize(path), 0,
+                                   "save_to_file must have written to the KG_PATH file")
+
+                # Simulate restart: reload into a fresh graph.
+                g2 = ContextGraph(advanced_analytics=False)
+                g2.load_from_file(path)
+                decisions = list(g2.find_nodes(node_type="decision"))
+                self.assertGreater(len(decisions), 0,
+                                   "Decision must be present after save → load")
+                cats = [d.get("category") or (d.get("metadata") or {}).get("category")
+                        for d in decisions]
+                self.assertIn("mcp_server_persist", cats)
+            finally:
+                os.unlink(path)
+        finally:
+            self._restore_mcp_graph()
+
+    def test_record_decision_works_without_kg_path(self):
+        """_tool_record_decision must succeed when SEMANTICA_KG_PATH is unset."""
+        from semantica.mcp_server import _tool_record_decision
+
+        g = self._isolated_mcp_graph()
+        try:
+            env = {k: v for k, v in os.environ.items() if k != "SEMANTICA_KG_PATH"}
+            with patch.dict(os.environ, env, clear=True):
+                result = _tool_record_decision({
+                    "category": "no_path",
+                    "scenario": "no kg path",
+                    "reasoning": "in-memory only",
+                    "outcome": "ok",
+                    "confidence": 0.5,
+                })
+            self.assertNotIn("error", result, result)
+            self.assertIn("decision_id", result)
+        finally:
+            self._restore_mcp_graph()
+
+    # ---- add_entity -----------------------------------------------------
+
+    def test_add_entity_persists_to_kg_path(self):
+        """_tool_add_entity must write the graph to SEMANTICA_KG_PATH."""
+        from semantica.mcp_server import _tool_add_entity
+
+        g = self._isolated_mcp_graph()
+        try:
+            with tempfile.NamedTemporaryFile(suffix=".json", delete=False) as f:
+                path = f.name
+            try:
+                with patch.dict(os.environ, {"SEMANTICA_KG_PATH": path}):
+                    result = _tool_add_entity({
+                        "id": "mcp_server_entity_test",
+                        "label": "Persistence Entity",
+                        "type": "TestEntity",
+                    })
+
+                self.assertNotIn("error", result, result)
+                self.assertEqual(result.get("status"), "added")
+
+                self.assertGreater(os.path.getsize(path), 0)
+
+                g2 = ContextGraph(advanced_analytics=False)
+                g2.load_from_file(path)
+                self.assertTrue(g2.has_node("mcp_server_entity_test"),
+                                "Entity must be present after save → load")
+            finally:
+                os.unlink(path)
+        finally:
+            self._restore_mcp_graph()
+
+    def test_add_entity_works_without_kg_path(self):
+        """_tool_add_entity must succeed when SEMANTICA_KG_PATH is unset."""
+        from semantica.mcp_server import _tool_add_entity
+
+        g = self._isolated_mcp_graph()
+        try:
+            env = {k: v for k, v in os.environ.items() if k != "SEMANTICA_KG_PATH"}
+            with patch.dict(os.environ, env, clear=True):
+                result = _tool_add_entity({"id": "ephemeral_ent", "label": "E"})
+            self.assertNotIn("error", result, result)
+            self.assertEqual(result.get("status"), "added")
+        finally:
+            self._restore_mcp_graph()
+
+    # ---- add_relationship -----------------------------------------------
+
+    def test_add_relationship_persists_to_kg_path(self):
+        """_tool_add_relationship must write the graph to SEMANTICA_KG_PATH."""
+        from semantica.mcp_server import _tool_add_entity, _tool_add_relationship
+
+        g = self._isolated_mcp_graph()
+        try:
+            with tempfile.NamedTemporaryFile(suffix=".json", delete=False) as f:
+                path = f.name
+            try:
+                with patch.dict(os.environ, {"SEMANTICA_KG_PATH": path}):
+                    _tool_add_entity({"id": "rel_src_mcp", "label": "Source"})
+                    _tool_add_entity({"id": "rel_tgt_mcp", "label": "Target"})
+                    result = _tool_add_relationship({
+                        "source": "rel_src_mcp",
+                        "target": "rel_tgt_mcp",
+                        "type": "PROVEN_BY",
+                    })
+
+                self.assertNotIn("error", result, result)
+                self.assertEqual(result.get("status"), "added")
+
+                self.assertGreater(os.path.getsize(path), 0)
+
+                g2 = ContextGraph(advanced_analytics=False)
+                g2.load_from_file(path)
+                edges = list(g2.find_edges())
+                self.assertTrue(any(e.get("type") == "PROVEN_BY" for e in edges),
+                                "PROVEN_BY edge must be present after save → load")
+            finally:
+                os.unlink(path)
+        finally:
+            self._restore_mcp_graph()
+
+    def test_add_relationship_works_without_kg_path(self):
+        """_tool_add_relationship must succeed when SEMANTICA_KG_PATH is unset."""
+        from semantica.mcp_server import _tool_add_entity, _tool_add_relationship
+
+        g = self._isolated_mcp_graph()
+        try:
+            env = {k: v for k, v in os.environ.items() if k != "SEMANTICA_KG_PATH"}
+            with patch.dict(os.environ, env, clear=True):
+                _tool_add_entity({"id": "src_no_p", "label": "S"})
+                _tool_add_entity({"id": "tgt_no_p", "label": "T"})
+                result = _tool_add_relationship({
+                    "source": "src_no_p",
+                    "target": "tgt_no_p",
+                    "type": "RELATED_TO",
+                })
+            self.assertNotIn("error", result, result)
+            self.assertEqual(result.get("status"), "added")
+        finally:
+            self._restore_mcp_graph()
+
+
 if __name__ == "__main__":
     unittest.main()

tests/test_mcp_package_persistence.py

@@ -0,0 +1,294 @@
+"""Regression tests for root mcp/ graph persistence (issue #1134).
+
+Covers:
+  1. get_graph() loads an existing JSON file via load_from_file(), not the
+     nonexistent .load() method  (the original bug).
+  2. get_graph() with a nonexistent / unset SEMANTICA_KG_PATH starts cleanly.
+  3. handle_record_decision persists to SEMANTICA_KG_PATH and the mutation
+     survives a fresh load_from_file() call.
+  4. handle_add_entity persists to SEMANTICA_KG_PATH and survives reload.
+  5. handle_add_relationship persists to SEMANTICA_KG_PATH and survives reload.
+  6. All three mutation tools work correctly when SEMANTICA_KG_PATH is unset
+     (no errors, no persistence attempt).
+"""
+
+from __future__ import annotations
+
+import os
+import tempfile
+import unittest
+from unittest.mock import patch
+
+from semantica.context.context_graph import ContextGraph
+
+import mcp.session as _session
+
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+def _fresh_graph() -> ContextGraph:
+    """Return a minimal ContextGraph ready for use in tests."""
+    g = ContextGraph(advanced_analytics=False)
+    g.add_node("seed_node", node_type="entity", label="Seed")
+    return g
+
+
+class _IsolatedSession:
+    """Context manager that resets the mcp.session singleton before and after
+    each test so tests are independent of process-level state."""
+
+    def __enter__(self):
+        _session.reset_graph()
+        return self
+
+    def __exit__(self, *_):
+        _session.reset_graph()
+
+
+# ---------------------------------------------------------------------------
+# 1. get_graph() loading — regression against _graph.load()
+# ---------------------------------------------------------------------------
+
+class TestMCPSessionLoad(unittest.TestCase):
+    """get_graph() must load an existing file using load_from_file(), not .load()."""
+
+    def test_get_graph_loads_existing_kg_path(self):
+        """When SEMANTICA_KG_PATH points to a valid JSON file the graph must
+        contain the persisted nodes after get_graph() returns."""
+        g = _fresh_graph()
+        g.add_node("persistent_node", node_type="entity", label="Should survive")
+
+        with tempfile.NamedTemporaryFile(suffix=".json", delete=False) as f:
+            path = f.name
+        try:
+            g.save_to_file(path)
+
+            with _IsolatedSession():
+                with patch.dict(os.environ, {"SEMANTICA_KG_PATH": path}):
+                    loaded = _session.get_graph()
+
+                self.assertTrue(
+                    loaded.has_node("persistent_node"),
+                    "Node saved before server start must be present after load",
+                )
+                self.assertTrue(
+                    loaded.has_node("seed_node"),
+                    "seed_node from the persisted graph must also be present",
+                )
+        finally:
+            os.unlink(path)
+
+    def test_get_graph_with_nonexistent_kg_path_starts_empty(self):
+        """When SEMANTICA_KG_PATH does not exist the graph initialises empty
+        (no error) — matching pre-existing behaviour."""
+        with _IsolatedSession():
+            with patch.dict(os.environ, {"SEMANTICA_KG_PATH": "/nonexistent/path.json"}):
+                loaded = _session.get_graph()
+
+        # An empty graph has no nodes; at minimum it must be a ContextGraph.
+        self.assertIsNotNone(loaded)
+        nodes = list(loaded.find_nodes())
+        self.assertEqual(nodes, [], "Graph must be empty when KG_PATH does not exist")
+
+    def test_get_graph_without_kg_path_starts_empty(self):
+        """When SEMANTICA_KG_PATH is absent the graph initialises empty."""
+        with _IsolatedSession():
+            env = {k: v for k, v in os.environ.items() if k != "SEMANTICA_KG_PATH"}
+            with patch.dict(os.environ, env, clear=True):
+                loaded = _session.get_graph()
+
+        self.assertIsNotNone(loaded)
+
+    def test_get_graph_uses_load_from_file_not_load(self):
+        """Regression: ContextGraph has no .load() method; get_graph() must
+        call load_from_file() or the AttributeError is silently swallowed and
+        the graph silently stays empty.  This test verifies the fix directly."""
+        g = _fresh_graph()
+        with tempfile.NamedTemporaryFile(suffix=".json", delete=False) as f:
+            path = f.name
+        try:
+            g.save_to_file(path)
+
+            with _IsolatedSession():
+                with patch.dict(os.environ, {"SEMANTICA_KG_PATH": path}):
+                    # If the old _graph.load(path) bug were present the graph
+                    # would be empty (exception swallowed).  With the fix the
+                    # node must be present.
+                    loaded = _session.get_graph()
+
+                self.assertTrue(
+                    loaded.has_node("seed_node"),
+                    "load_from_file must have been called; if .load() was used "
+                    "the AttributeError is swallowed and the graph stays empty",
+                )
+        finally:
+            os.unlink(path)
+
+
+# ---------------------------------------------------------------------------
+# 2–5. Mutation persistence
+# ---------------------------------------------------------------------------
+
+class TestMCPPackageMutationPersistence(unittest.TestCase):
+    """Mutations via the root mcp/ tool handlers must persist to SEMANTICA_KG_PATH
+    so the data survives a server restart (simulated by a fresh load_from_file)."""
+
+    # ---- record_decision ------------------------------------------------
+
+    def test_record_decision_persists_when_kg_path_set(self):
+        """handle_record_decision must write to disk when SEMANTICA_KG_PATH is set."""
+        from mcp.tools.decisions import handle_record_decision
+
+        with tempfile.NamedTemporaryFile(suffix=".json", delete=False) as f:
+            path = f.name
+        try:
+            with _IsolatedSession():
+                with patch.dict(os.environ, {"SEMANTICA_KG_PATH": path}):
+                    result = handle_record_decision({
+                        "category": "test_persistence",
+                        "scenario": "Verifying mcp/ decision persistence",
+                        "reasoning": "KG_PATH must be written on mutation",
+                        "outcome": "verified",
+                        "confidence": 0.99,
+                    })
+
+            self.assertNotIn("error", result, result)
+            self.assertIn("decision_id", result)
+
+            # The file must have been written (or overwritten from empty).
+            self.assertTrue(os.path.exists(path), "save_to_file must create the file")
+            self.assertGreater(os.path.getsize(path), 0, "Persisted file must not be empty")
+
+            # Simulate server restart: load into a fresh graph.
+            g2 = ContextGraph(advanced_analytics=False)
+            g2.load_from_file(path)
+            decisions = list(g2.find_nodes(node_type="decision"))
+            self.assertGreater(len(decisions), 0, "Decision must survive reload")
+            cats = [d.get("category") or (d.get("metadata") or {}).get("category")
+                    for d in decisions]
+            self.assertIn("test_persistence", cats,
+                          "Decision category must be present after reload")
+        finally:
+            os.unlink(path)
+
+    def test_record_decision_works_without_kg_path(self):
+        """handle_record_decision must succeed even when SEMANTICA_KG_PATH is unset."""
+        from mcp.tools.decisions import handle_record_decision
+
+        with _IsolatedSession():
+            env = {k: v for k, v in os.environ.items() if k != "SEMANTICA_KG_PATH"}
+            with patch.dict(os.environ, env, clear=True):
+                result = handle_record_decision({
+                    "category": "no_path",
+                    "scenario": "No persistence path configured",
+                    "reasoning": "Should still work in-memory",
+                    "outcome": "ok",
+                    "confidence": 0.5,
+                })
+
+        self.assertNotIn("error", result, result)
+        self.assertIn("decision_id", result)
+
+    # ---- add_entity -----------------------------------------------------
+
+    def test_add_entity_persists_when_kg_path_set(self):
+        """handle_add_entity must write to disk when SEMANTICA_KG_PATH is set."""
+        from mcp.tools.graph import handle_add_entity
+
+        with tempfile.NamedTemporaryFile(suffix=".json", delete=False) as f:
+            path = f.name
+        try:
+            with _IsolatedSession():
+                with patch.dict(os.environ, {"SEMANTICA_KG_PATH": path}):
+                    result = handle_add_entity({
+                        "id": "entity_persist_test",
+                        "label": "Persistence Test Entity",
+                        "type": "TestType",
+                    })
+
+            self.assertNotIn("error", result, result)
+            self.assertEqual(result.get("status"), "added")
+
+            self.assertTrue(os.path.exists(path))
+            self.assertGreater(os.path.getsize(path), 0)
+
+            g2 = ContextGraph(advanced_analytics=False)
+            g2.load_from_file(path)
+            self.assertTrue(
+                g2.has_node("entity_persist_test"),
+                "Entity must be present in the graph after reload",
+            )
+        finally:
+            os.unlink(path)
+
+    def test_add_entity_works_without_kg_path(self):
+        """handle_add_entity must succeed when SEMANTICA_KG_PATH is unset."""
+        from mcp.tools.graph import handle_add_entity
+
+        with _IsolatedSession():
+            env = {k: v for k, v in os.environ.items() if k != "SEMANTICA_KG_PATH"}
+            with patch.dict(os.environ, env, clear=True):
+                result = handle_add_entity({"id": "no_path_entity", "label": "ephemeral"})
+
+        self.assertNotIn("error", result, result)
+        self.assertEqual(result.get("status"), "added")
+
+    # ---- add_relationship -----------------------------------------------
+
+    def test_add_relationship_persists_when_kg_path_set(self):
+        """handle_add_relationship must write to disk when SEMANTICA_KG_PATH is set."""
+        from mcp.tools.graph import handle_add_relationship
+
+        with tempfile.NamedTemporaryFile(suffix=".json", delete=False) as f:
+            path = f.name
+        try:
+            with _IsolatedSession():
+                with patch.dict(os.environ, {"SEMANTICA_KG_PATH": path}):
+                    # Nodes must exist before an edge can be added.
+                    from mcp.tools.graph import handle_add_entity
+                    handle_add_entity({"id": "rel_src", "label": "Source"})
+                    handle_add_entity({"id": "rel_tgt", "label": "Target"})
+                    result = handle_add_relationship({
+                        "source": "rel_src",
+                        "target": "rel_tgt",
+                        "type": "TESTED_BY",
+                    })
+
+            self.assertNotIn("error", result, result)
+            self.assertEqual(result.get("status"), "added")
+
+            self.assertTrue(os.path.exists(path))
+            self.assertGreater(os.path.getsize(path), 0)
+
+            g2 = ContextGraph(advanced_analytics=False)
+            g2.load_from_file(path)
+            edges = list(g2.find_edges())
+            edge_types = [e.get("type") for e in edges]
+            self.assertIn("TESTED_BY", edge_types,
+                          "Relationship must be present after reload")
+        finally:
+            os.unlink(path)
+
+    def test_add_relationship_works_without_kg_path(self):
+        """handle_add_relationship must succeed when SEMANTICA_KG_PATH is unset."""
+        from mcp.tools.graph import handle_add_entity, handle_add_relationship
+
+        with _IsolatedSession():
+            env = {k: v for k, v in os.environ.items() if k != "SEMANTICA_KG_PATH"}
+            with patch.dict(os.environ, env, clear=True):
+                handle_add_entity({"id": "src_no_path", "label": "S"})
+                handle_add_entity({"id": "tgt_no_path", "label": "T"})
+                result = handle_add_relationship({
+                    "source": "src_no_path",
+                    "target": "tgt_no_path",
+                    "type": "RELATED_TO",
+                })
+
+        self.assertNotIn("error", result, result)
+        self.assertEqual(result.get("status"), "added")
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_mcp_stdio_roundtrip.py

@@ -0,0 +1,180 @@
+"""MCP stdio JSON-RPC framing regression test (#1134, point 1).
+
+The original bug: progress output from the Semantica progress tracker was
+written to sys.stdout, which is also the MCP JSON-RPC transport channel.
+Interleaving progress text with JSON-RPC responses made every response
+unparseable and hung the client.
+
+These tests exercise the *actual* root mcp/ server stdio framing loop
+(SemanticaMCPServer.run()) over a real subprocess pipe, not just the handler
+layer.  They prove that:
+
+  1. Every non-empty stdout line produced by the running server is valid JSON.
+  2. A valid JSON-RPC response is received for each request sent.
+  3. No progress / non-JSON bytes appear on stdout even when a tool triggers
+     the progress-producing code path (constructing a ContextGraph, which
+     calls get_progress_tracker() and attempts to enable the tracker).
+
+Tests that are already covered elsewhere are not duplicated here:
+  - ConsoleProgressDisplay writing to stderr (test_progress_stream.py)
+  - SEMANTICA_DISABLE_PROGRESS blocking re-enable (test_progress_tracker_regressions.py)
+  - mcp import sets SEMANTICA_DISABLE_PROGRESS (test_mcp_package_export_graph.py)
+"""
+
+from __future__ import annotations
+
+import json
+import os
+import subprocess
+import sys
+import unittest
+
+
+# ---------------------------------------------------------------------------
+# Module-level helpers
+# ---------------------------------------------------------------------------
+
+def _repo_root() -> str:
+    return os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
+
+
+def _subprocess_env() -> dict[str, str]:
+    """Clean env with the repo on PYTHONPATH and no pre-set progress flag."""
+    env = os.environ.copy()
+    env["PYTHONPATH"] = _repo_root()
+    env.pop("SEMANTICA_DISABLE_PROGRESS", None)
+    return env
+
+
+def _jsonrpc(method: str, req_id: int | None, params: dict | None = None) -> bytes:
+    msg: dict = {"jsonrpc": "2.0", "method": method}
+    if req_id is not None:
+        msg["id"] = req_id
+    if params is not None:
+        msg["params"] = params
+    return (json.dumps(msg) + "\n").encode()
+
+
+def _assert_stdout_is_clean_json(test: unittest.TestCase,
+                                  stdout: str,
+                                  stderr: str = "") -> list[dict]:
+    """Assert every non-empty stdout line is valid JSON; return parsed objects.
+
+    Fails immediately with a useful diagnostic if any line is not JSON.
+    """
+    lines = [ln for ln in stdout.splitlines() if ln.strip()]
+    test.assertGreater(
+        len(lines), 0,
+        f"Expected at least one stdout line but got none.\nstderr={stderr!r}",
+    )
+    parsed = []
+    for i, line in enumerate(lines):
+        try:
+            parsed.append(json.loads(line))
+        except json.JSONDecodeError as exc:
+            test.fail(
+                f"stdout line {i} is not valid JSON (regression: progress leaked "
+                f"to stdout?)\n  line: {line!r}\n  error: {exc}\n  stderr={stderr!r}"
+            )
+    return parsed
+
+
+_INIT_REQUEST = _jsonrpc("initialize", 1, {
+    "protocolVersion": "2024-11-05",
+    "clientInfo": {"name": "test", "version": "0"},
+    "capabilities": {},
+})
+
+
+# ---------------------------------------------------------------------------
+# Main regression suite
+# ---------------------------------------------------------------------------
+
+class TestMCPStdioFramingContract(unittest.TestCase):
+    """Run 'python -m mcp' exactly as an MCP client would, over a real pipe.
+
+    Each test sends a complete JSON-RPC session through stdin and asserts that
+    every byte on stdout is valid JSON — catching the exact failure mode from
+    #1134 where progress output corrupted the transport stream.
+    """
+
+    TIMEOUT = 30
+
+    def _run(self, *requests: bytes) -> subprocess.CompletedProcess:
+        return subprocess.run(
+            [sys.executable, "-m", "mcp"],
+            input=b"".join(requests),
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            timeout=self.TIMEOUT,
+            cwd=_repo_root(),
+            env=_subprocess_env(),
+            check=False,
+        )
+
+    # ------------------------------------------------------------------
+
+    def test_initialize_stdout_is_valid_json_rpc(self):
+        """An initialize request must produce a single valid JSON-RPC response."""
+        proc = self._run(_INIT_REQUEST)
+
+        self.assertEqual(proc.returncode, 0,
+                         f"server crashed:\n{proc.stderr.decode()}")
+        responses = _assert_stdout_is_clean_json(
+            self, proc.stdout.decode(), proc.stderr.decode()
+        )
+        init_resp = next((r for r in responses if r.get("id") == 1), None)
+        self.assertIsNotNone(init_resp, f"No id=1 response in: {responses}")
+        self.assertIn("serverInfo", init_resp.get("result", {}))
+
+    def test_tools_call_stdout_is_clean_json_rpc(self):
+        """A tools/call round-trip through the full stdio framing loop must keep
+        stdout free of any non-JSON bytes.
+
+        run_reasoning is used because Reasoner.infer_with_results() explicitly
+        calls self.progress_tracker.start_tracking(), making it the minimal
+        deterministic tool path that exercises the progress-rendering code.
+        Before the #1134 fix, that start_tracking call wrote a progress bar
+        directly to stdout, corrupting the JSON-RPC framing.  Every byte on
+        stdout must still be valid JSON-RPC after the fix.
+        """
+        proc = self._run(
+            _INIT_REQUEST,
+            _jsonrpc("notifications/initialized", None),
+            _jsonrpc("tools/call", 2, {
+                "name": "run_reasoning",
+                "arguments": {
+                    "facts": ["Person(Alice)", "Employee(Alice)"],
+                    "rules": ["IF Employee(?x) THEN Worker(?x)"],
+                },
+            }),
+        )
+        self.assertEqual(proc.returncode, 0,
+                         f"server crashed:\n{proc.stderr.decode()}")
+
+        stdout = proc.stdout.decode()
+        stderr = proc.stderr.decode()
+        responses = _assert_stdout_is_clean_json(self, stdout, stderr)
+
+        tool_resp = next((r for r in responses if r.get("id") == 2), None)
+        self.assertIsNotNone(
+            tool_resp,
+            f"No id=2 response in stdout.\nstdout={stdout!r}\nstderr={stderr!r}",
+        )
+        # The framing must be a valid JSON-RPC result object regardless of
+        # whether the reasoner dependency is available in this environment.
+        self.assertIn("jsonrpc", tool_resp)
+        self.assertEqual(tool_resp["jsonrpc"], "2.0")
+        self.assertIn("id", tool_resp)
+        # If the tool succeeded the response must carry MCP content.
+        if "result" in tool_resp:
+            content = tool_resp["result"].get("content", [])
+            self.assertGreater(len(content), 0,
+                               "Expected non-empty content list in result")
+            # The embedded tool payload must itself be valid JSON.
+            inner = json.loads(content[0]["text"])
+            self.assertIn("derived_facts", inner)
+
+
+if __name__ == "__main__":
+    unittest.main()