sysprom 1.13.2 → 1.15.0

package/dist/src/json-to-md.js

@@ -22,6 +22,58 @@ function renderFrontMatter(fields) {
     lines.push("---");
     return lines.join("\n");
 }
+// ---------------------------------------------------------------------------
+// Node location map (for hyperlinking)
+// ---------------------------------------------------------------------------
+/** GitHub-compatible heading anchor slug. */
+function slugify(text) {
+    return text
+        .toLowerCase()
+        .replace(/[^\w\s-]/g, "")
+        .replace(/\s/g, "-");
+}
+/** Heading anchor for a node: `id--name` slugified from `### ID — Name`. */
+function nodeAnchor(n) {
+    return slugify(`${n.id} — ${n.name}`);
+}
+/** Build a map from node ID to its markdown file and heading anchor. */
+function buildNodeLocationMap(nodes, mode) {
+    const map = new Map();
+    for (const n of nodes) {
+        const anchor = nodeAnchor(n);
+        if (mode === "single-file") {
+            map.set(n.id, { file: "", anchor });
+        }
+        else {
+            const file = fileForNodeType(n.type);
+            map.set(n.id, { file, anchor });
+        }
+    }
+    return map;
+}
+/** Determine the markdown file a node type belongs to in multi-doc mode. */
+function fileForNodeType(type) {
+    for (const [fileName, types] of Object.entries(NODE_FILE_MAP)) {
+        if (types.includes(type))
+            return `${fileName}.md`;
+    }
+    return "README.md";
+}
+/**
+ * Format a node ID as a markdown hyperlink.
+ * In single-file mode: `[ID](#anchor)`
+ * In multi-doc mode: `[ID](./FILE.md#anchor)`
+ * Falls back to plain ID if the node isn't in the map.
+ */
+function linkNodeId(id, nodeMap, currentFile) {
+    const loc = nodeMap.get(id);
+    if (!loc)
+        return id;
+    if (loc.file === "" || loc.file === currentFile) {
+        return `[${id}](#${loc.anchor})`;
+    }
+    return `[${id}](./${loc.file}#${loc.anchor})`;
+}
 function indexRelationshipsFrom(rels) {
     const idx = new Map();
     for (const r of rels) {
@@ -79,7 +131,7 @@ function renderLifecycle(lifecycle) {
         return `- [${checkbox}] ${label}`;
     });
 }
-function renderNodeRelationships(nodeId, fromIdx) {
+function renderNodeRelationships(nodeId, fromIdx, nodeMap, currentFile) {
     const rels = fromIdx.get(nodeId);
     if (!rels || rels.length === 0)
         return [];
@@ -97,12 +149,12 @@ function renderNodeRelationships(nodeId, fromIdx) {
             ? RELATIONSHIP_TYPE_LABELS[type]
             : type;
         if (targets.length === 1) {
-            lines.push(`- ${label}: ${targets[0]}`);
+            lines.push(`- ${label}: ${linkNodeId(targets[0], nodeMap, currentFile)}`);
         }
         else {
             lines.push(`- ${label}:`);
             for (const t of targets) {
-                lines.push(`  - ${t}`);
+                lines.push(`  - ${linkNodeId(t, nodeMap, currentFile)}`);
             }
         }
     }
@@ -123,7 +175,7 @@ function renderExternalReferences(refs) {
     }
     return lines;
 }
-function renderNode(n, headingLevel, fromIdx) {
+function renderNode(n, headingLevel, fromIdx, nodeMap, currentFile) {
     const prefix = "#".repeat(headingLevel);
     const lines = [];
     lines.push(`${prefix} ${n.id} — ${n.name}`);
@@ -132,7 +184,7 @@ function renderNode(n, headingLevel, fromIdx) {
         lines.push(renderText(n.description));
         lines.push("");
     }
-    const rels = renderNodeRelationships(n.id, fromIdx);
+    const rels = renderNodeRelationships(n.id, fromIdx, nodeMap, currentFile);
     if (rels.length > 0) {
         lines.push(...rels);
         lines.push("");
@@ -207,7 +259,7 @@ function renderNode(n, headingLevel, fromIdx) {
     if (n.includes && n.includes.length > 0) {
         lines.push("Includes:");
         for (const inc of n.includes) {
-            lines.push(`- ${inc}`);
+            lines.push(`- ${linkNodeId(inc, nodeMap, currentFile)}`);
         }
         lines.push("");
     }
@@ -233,8 +285,9 @@ function renderNode(n, headingLevel, fromIdx) {
         const subNodes = n.subsystem.nodes;
         const subRels = n.subsystem.relationships ?? [];
         const subIdx = indexRelationshipsFrom(subRels);
+        const subMap = buildNodeLocationMap(subNodes, "single-file");
         for (const sub of subNodes) {
-            lines.push(...renderNode(sub, headingLevel + 2, subIdx));
+            lines.push(...renderNode(sub, headingLevel + 2, subIdx, subMap));
         }
     }
     return lines;
@@ -242,7 +295,7 @@ function renderNode(n, headingLevel, fromIdx) {
 // ---------------------------------------------------------------------------
 // File generators
 // ---------------------------------------------------------------------------
-function renderNodesGrouped(nodes, types, fromIdx, headingLevel) {
+function renderNodesGrouped(nodes, types, fromIdx, headingLevel, nodeMap, currentFile) {
     const lines = [];
     for (const type of types) {
         const matching = nodes.filter((n) => n.type === type);
@@ -252,12 +305,12 @@ function renderNodesGrouped(nodes, types, fromIdx, headingLevel) {
         lines.push(`${"#".repeat(headingLevel)} ${label}`);
         lines.push("");
         for (const n of matching) {
-            lines.push(...renderNode(n, headingLevel + 1, fromIdx));
+            lines.push(...renderNode(n, headingLevel + 1, fromIdx, nodeMap, currentFile));
         }
     }
     return lines;
 }
-function generateReadme(doc, fromIdx) {
+function generateReadme(doc, fromIdx, nodeMap) {
     const lines = [];
     const title = doc.metadata?.title ?? "SysProM";
     lines.push(renderFrontMatter({
@@ -329,7 +382,7 @@ function generateReadme(doc, fromIdx) {
     // Views
     const views = doc.nodes.filter((n) => n.type === "view");
     if (views.length > 0) {
-        lines.push(...renderNodesGrouped(doc.nodes, ["view"], fromIdx, 2));
+        lines.push(...renderNodesGrouped(doc.nodes, ["view"], fromIdx, 2, nodeMap, "README.md"));
     }
     // Graph-level external references
     if (doc.external_references && doc.external_references.length > 0) {
@@ -347,7 +400,7 @@ function generateReadme(doc, fromIdx) {
     }
     return lines.join("\n") + "\n";
 }
-function generateDocFile(doc, fileName, types, fromIdx) {
+function generateDocFile(doc, fileName, types, fromIdx, nodeMap) {
     const lines = [];
     lines.push(renderFrontMatter({
         title: fileName.replace(".md", ""),
@@ -356,7 +409,7 @@ function generateDocFile(doc, fileName, types, fromIdx) {
     lines.push("");
     lines.push(`# ${fileName.replace(".md", "")}`);
     lines.push("");
-    lines.push(...renderNodesGrouped(doc.nodes, types, fromIdx, 2));
+    lines.push(...renderNodesGrouped(doc.nodes, types, fromIdx, 2, nodeMap, `${fileName}.md`));
     return lines.join("\n") + "\n";
 }
 /**
@@ -371,6 +424,7 @@ function generateDocFile(doc, fileName, types, fromIdx) {
  */
 export function jsonToMarkdownSingle(doc) {
     const fromIdx = indexRelationshipsFrom(doc.relationships ?? []);
+    const nodeMap = buildNodeLocationMap(doc.nodes, "single-file");
     const lines = [];
     const title = doc.metadata?.title ?? "SysProM";
     lines.push(renderFrontMatter({
@@ -394,7 +448,7 @@ export function jsonToMarkdownSingle(doc) {
         "milestone",
         "version",
     ];
-    lines.push(...renderNodesGrouped(doc.nodes, allTypes, fromIdx, 2));
+    lines.push(...renderNodesGrouped(doc.nodes, allTypes, fromIdx, 2, nodeMap));
     // Relationships summary
     if (doc.relationships && doc.relationships.length > 0) {
         lines.push("## Relationships");
@@ -433,12 +487,13 @@ export function jsonToMarkdownSingle(doc) {
 export function jsonToMarkdownMultiDoc(doc, outDir) {
     mkdirSync(outDir, { recursive: true });
     const fromIdx = indexRelationshipsFrom(doc.relationships ?? []);
-    writeFileSync(join(outDir, "README.md"), generateReadme(doc, fromIdx));
+    const nodeMap = buildNodeLocationMap(doc.nodes, "multi-doc");
+    writeFileSync(join(outDir, "README.md"), generateReadme(doc, fromIdx, nodeMap));
     for (const [fileName, types] of Object.entries(NODE_FILE_MAP)) {
         const hasNodes = doc.nodes.some((n) => types.includes(n.type));
         if (!hasNodes)
             continue;
-        writeFileSync(join(outDir, `${fileName}.md`), generateDocFile(doc, fileName, types, fromIdx));
+        writeFileSync(join(outDir, `${fileName}.md`), generateDocFile(doc, fileName, types, fromIdx, nodeMap));
     }
     // Subsystem folders or single files
     const subsystemNodes = doc.nodes.filter((n) => n.subsystem);

package/dist/src/mcp/server.js

@@ -2,9 +2,9 @@
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import * as z from "zod";
-import { loadDocument } from "../io.js";
+import { loadDocument, saveDocument } from "../io.js";
 import { NodeType, RelationshipType } from "../schema.js";
-import { validateOp, statsOp, queryNodesOp, queryNodeOp, queryRelationshipsOp, traceFromNodeOp, addNodeOp, removeNodeOp, updateNodeOp, addRelationshipOp, removeRelationshipOp, nextIdOp, } from "../operations/index.js";
+import { validateOp, statsOp, queryNodesOp, queryNodeOp, queryRelationshipsOp, traceFromNodeOp, addNodeOp, removeNodeOp, updateNodeOp, addRelationshipOp, removeRelationshipOp, nextIdOp, inferCompletenessOp, inferLifecycleOp, inferImpactOp, inferDerivedOp, } from "../operations/index.js";
 // Create MCP server instance
 const server = new McpServer({
     name: "sysprom-mcp",
@@ -145,14 +145,14 @@ server.registerTool("add-node", {
         description: z.string().optional().describe("Node description"),
     }),
 }, ({ path, type, id, name, description }) => {
-    const { doc } = loadDocument(path);
+    const loaded = loadDocument(path);
     const nodeType = NodeType.safeParse(type);
     if (!nodeType.success) {
         throw new Error(`Invalid node type: "${type}". Valid types: ${NodeType.options.join(", ")}`);
     }
-    const nodeId = id ?? nextIdOp({ doc, type: nodeType.data });
+    const nodeId = id ?? nextIdOp({ doc: loaded.doc, type: nodeType.data });
     const updated = addNodeOp({
-        doc,
+        doc: loaded.doc,
         node: {
             id: nodeId,
             type: nodeType.data,
@@ -160,6 +160,7 @@ server.registerTool("add-node", {
             ...(description && { description }),
         },
     });
+    saveDocument(updated, loaded.format, loaded.path);
     return {
         content: [
             {
@@ -181,8 +182,9 @@ server.registerTool("remove-node", {
         id: z.string().describe("Node ID"),
     }),
 }, ({ path, id }) => {
-    const { doc } = loadDocument(path);
-    const result = removeNodeOp({ doc, id });
+    const loaded = loadDocument(path);
+    const result = removeNodeOp({ doc: loaded.doc, id });
+    saveDocument(result.doc, loaded.format, loaded.path);
     return {
         content: [
             {
@@ -205,7 +207,7 @@ server.registerTool("update-node", {
         fields: z.record(z.string(), z.unknown()).describe("Fields to update"),
     }),
 }, ({ path, id, fields }) => {
-    const { doc } = loadDocument(path);
+    const loaded = loadDocument(path);
     // Validate fields are valid node property updates
     const validFields = Object.entries(fields).reduce((acc, [key, value]) => {
         // Allow common node fields; unknown fields are silently ignored
@@ -231,10 +233,11 @@ server.registerTool("update-node", {
         return acc;
     }, {});
     const updated = updateNodeOp({
-        doc,
+        doc: loaded.doc,
         id,
         fields: validFields,
     });
+    saveDocument(updated, loaded.format, loaded.path);
     const node = updated.nodes.find((n) => n.id === id);
     return {
         content: [
@@ -255,19 +258,20 @@ server.registerTool("add-relationship", {
         type: z.string().describe("Relationship type"),
     }),
 }, ({ path, from, to, type }) => {
-    const { doc } = loadDocument(path);
+    const loaded = loadDocument(path);
     const relType = RelationshipType.safeParse(type);
     if (!relType.success) {
         throw new Error(`Invalid relationship type: "${type}". Valid types: ${RelationshipType.options.join(", ")}`);
     }
     const updated = addRelationshipOp({
-        doc,
+        doc: loaded.doc,
         rel: {
             from,
             to,
             type: relType.data,
         },
     });
+    saveDocument(updated, loaded.format, loaded.path);
     return {
         content: [
             {
@@ -290,17 +294,18 @@ server.registerTool("remove-relationship", {
         type: z.string().describe("Relationship type"),
     }),
 }, ({ path, from, to, type }) => {
-    const { doc } = loadDocument(path);
+    const loaded = loadDocument(path);
     const relType = RelationshipType.safeParse(type);
     if (!relType.success) {
         throw new Error(`Invalid relationship type: "${type}". Valid types: ${RelationshipType.options.join(", ")}`);
     }
     const result = removeRelationshipOp({
-        doc,
+        doc: loaded.doc,
         from,
         to,
         type: relType.data,
     });
+    saveDocument(result.doc, loaded.format, loaded.path);
     return {
         content: [
             {
@@ -313,6 +318,79 @@ server.registerTool("remove-relationship", {
         ],
     };
 });
+// Register infer-completeness tool
+server.registerTool("infer-completeness", {
+    description: "Infer completeness of nodes based on expected refinement relationships",
+    inputSchema: z.object({
+        path: z.string().describe("Path to SysProM file"),
+    }),
+}, ({ path }) => {
+    const { doc } = loadDocument(path);
+    const result = inferCompletenessOp({ doc });
+    return {
+        content: [
+            {
+                type: "text",
+                text: JSON.stringify(result, null, 2),
+            },
+        ],
+    };
+});
+// Register infer-lifecycle tool
+server.registerTool("infer-lifecycle", {
+    description: "Infer lifecycle state for nodes based on status and lifecycle fields",
+    inputSchema: z.object({
+        path: z.string().describe("Path to SysProM file"),
+    }),
+}, ({ path }) => {
+    const { doc } = loadDocument(path);
+    const result = inferLifecycleOp({ doc });
+    return {
+        content: [
+            {
+                type: "text",
+                text: JSON.stringify(result, null, 2),
+            },
+        ],
+    };
+});
+// Register infer-impact tool
+server.registerTool("infer-impact", {
+    description: "Infer impact from a node through the graph following impact relationships",
+    inputSchema: z.object({
+        path: z.string().describe("Path to SysProM file"),
+        startId: z.string().describe("Node ID to start impact analysis from"),
+    }),
+}, ({ path, startId }) => {
+    const { doc } = loadDocument(path);
+    const result = inferImpactOp({ doc, startId });
+    return {
+        content: [
+            {
+                type: "text",
+                text: JSON.stringify(result, null, 2),
+            },
+        ],
+    };
+});
+// Register infer-derived tool
+server.registerTool("infer-derived", {
+    description: "Infer derived relationships from transitive closure, inverses, and composites",
+    inputSchema: z.object({
+        path: z.string().describe("Path to SysProM file"),
+    }),
+}, ({ path }) => {
+    const { doc } = loadDocument(path);
+    const result = inferDerivedOp({ doc });
+    return {
+        content: [
+            {
+                type: "text",
+                text: JSON.stringify(result, null, 2),
+            },
+        ],
+    };
+});
 // Start server
 async function main() {
     const transport = new StdioServerTransport();

package/dist/src/md-to-json.js

@@ -2,6 +2,10 @@ import * as z from "zod";
 import { readFileSync, existsSync, readdirSync, statSync } from "node:fs";
 import { join, basename } from "node:path";
 import { NODE_FILE_MAP, NODE_LABEL_TO_TYPE, RELATIONSHIP_TYPE_LABELS, RELATIONSHIP_LABEL_TO_TYPE, NodeType, RelationshipType, NodeStatus, ExternalReferenceRole, } from "./schema.js";
+/** Strip markdown link syntax `[text](url)` → `text`. */
+function stripMarkdownLink(s) {
+    return s.replace(/\[([^\]]+)\]\([^)]+\)/g, "$1");
+}
 const LABEL_TO_TYPE = Object.fromEntries(Object.entries(NODE_LABEL_TO_TYPE).map(([k, v]) => [k.toLowerCase(), v]));
 const operationType = z.enum(["add", "update", "remove", "link"]);
 function parseNodeType(s) {
@@ -162,18 +166,18 @@ function parseListItems(body, prefix) {
             collecting = true;
             const inline = line.slice(prefix.length + 1).trim();
             if (inline) {
-                items.push(inline);
+                items.push(stripMarkdownLink(inline));
                 collecting = false;
             }
             continue;
         }
         if (collecting && line.startsWith("  - ")) {
-            items.push(line.slice(4));
+            items.push(stripMarkdownLink(line.slice(4)));
         }
         else if (collecting &&
             line.startsWith("- ") &&
             !isRelationshipLabel(line)) {
-            items.push(line.slice(2));
+            items.push(stripMarkdownLink(line.slice(2)));
         }
         else if (collecting) {
             collecting = false;
@@ -210,7 +214,7 @@ function parseRelationshipsFromBody(body, nodeId) {
         if (items.length === 0) {
             const val = parseSingleValue(body, `- ${label}`);
             if (val) {
-                rels.push({ from: nodeId, to: val, type: relType });
+                rels.push({ from: nodeId, to: stripMarkdownLink(val), type: relType });
             }
         }
         else {

package/dist/src/operations/index.d.ts

@@ -37,3 +37,7 @@ export { speckitImportOp } from "./speckit-import.js";
 export { speckitExportOp } from "./speckit-export.js";
 export { speckitSyncOp, type SyncResult } from "./speckit-sync.js";
 export { speckitDiffOp, type DiffResult } from "./speckit-diff.js";
+export { inferCompletenessOp, type CompletenessResult, type CompletenessOutput, } from "./infer-completeness.js";
+export { inferLifecycleOp, type LifecycleResult, type LifecycleOutput, } from "./infer-lifecycle.js";
+export { inferImpactOp, type ImpactNode, type ImpactOutput, } from "./infer-impact.js";
+export { inferDerivedOp, type DerivedRelationship, type DerivedOutput, } from "./infer-derived.js";

package/dist/src/operations/index.js

@@ -45,3 +45,8 @@ export { speckitImportOp } from "./speckit-import.js";
 export { speckitExportOp } from "./speckit-export.js";
 export { speckitSyncOp } from "./speckit-sync.js";
 export { speckitDiffOp } from "./speckit-diff.js";
+// Inference operations
+export { inferCompletenessOp, } from "./infer-completeness.js";
+export { inferLifecycleOp, } from "./infer-lifecycle.js";
+export { inferImpactOp, } from "./infer-impact.js";
+export { inferDerivedOp, } from "./infer-derived.js";