@gwdn/nexus-mcp 0.8.0 → 0.8.3

package/README.md

@@ -78,6 +78,31 @@ src/
   __tests__/         # Unit tests (112) and E2E integration tests (34)
 ```
 
+## Known Issues
+
+### npx cache prevents version upgrade
+
+When using `npx` to run the MCP server, npm caches the resolved package in
+`~/.npm/_npx/`. Subsequent invocations may continue to use the cached
+(outdated) version even after a new release is published — especially in
+terminals that were started before the update.
+
+**Symptoms:** MCP tools report an older version, or new tools/fixes are missing.
+
+**Fix:** Before starting OpenCode, clear stale npx caches:
+
+```bash
+find ~/.npm/_npx -path "*/node_modules/@gwdn/nexus-mcp/package.json" \
+  -exec node -e "if(require('{}').version!=='0.8.1') console.log(require('path').resolve('{}','../../..'))" \; \
+  | xargs rm -rf
+```
+
+Then start OpenCode normally. npx will fetch the latest version into a fresh
+cache entry.
+
+> **Tip:** To avoid this entirely, pin `@latest` in your MCP config args:
+> `["--yes", "@gwdn/nexus-mcp@latest"]`
+
 ## Related
 
 - [nexus](https://github.com/gwnexus/nexus-hub) — Backend + Frontend (Next.js/Supabase/Netlify)

package/dist/server.js

@@ -85,6 +85,9 @@ import { appendSessionEntry, appendSessionEntrySchema, } from './tools/append-se
 import { createTask, createTaskSchema } from './tools/create-task.js';
 import { addDecisionComment, addDecisionCommentSchema, listDecisionComments, listDecisionCommentsSchema, } from './tools/decision-comments.js';
 import { ingestDocument, ingestDocumentSchema, } from './tools/ingest-document.js';
+import { classifyDocument, classifyDocumentSchema, } from './tools/classify-document.js';
+import { updateDocument, updateDocumentSchema, } from './tools/update-document.js';
+import { deleteDocument, deleteDocumentSchema, } from './tools/delete-document.js';
 import { acknowledgeLetter, acknowledgeLetterSchema, listInbox, listInboxSchema, listOutbox, listOutboxSchema, } from './tools/letter-inbox.js';
 import { createLetter, createLetterSchema, replyLetter, replyLetterSchema, } from './tools/letters.js';
 import { listDocuments, listDocumentsSchema, } from './tools/list-documents.js';
@@ -146,6 +149,9 @@ server.tool('task_note', 'Append a note to an existing task. Notes are append-on
 server.tool('task_list', 'List tasks for a project with optional status filtering. Returns tasks ordered by creation date (newest first).', listTasksSchema, withIdentity(listTasks));
 server.tool('doc_ingest', 'Push text or markdown content into a project knowledge base. Creates an ingest item that can later be classified. Useful for agents to persist research results, generated documents, or extracted knowledge.', ingestDocumentSchema, withIdentity(ingestDocument));
 server.tool('doc_list', 'List ingested documents for a project with optional source filtering. Returns documents ordered by creation date (newest first).', listDocumentsSchema, withIdentity(listDocuments));
+server.tool('doc_classify', 'Update the classification of an ingest item. Valid classifications: unclassified, research_note, planning_item, decision_input, reference, archive.', classifyDocumentSchema, withIdentity(classifyDocument));
+server.tool('doc_update', 'Update title, body, or source_url of an ingest item. Supports full body replacement or append mode via append_body. At least one field must be provided.', updateDocumentSchema, withIdentity(updateDocument));
+server.tool('doc_delete', 'Delete an ingest item from a project knowledge base. This action is irreversible.', deleteDocumentSchema, withIdentity(deleteDocument));
 server.tool('session_append', 'Append an entry to an existing session. Enforces session write isolation: only the session creator can append entries.', appendSessionEntrySchema, withIdentity(appendSessionEntry));
 server.tool('session_create', 'Create a new work session for a project. Returns the session ID. The session starts in open status and must be closed explicitly via session_close.', createSessionSchema, withIdentity(createSession));
 server.tool('session_close', 'Close an open session. Sets status to closed, optionally records a summary and next entry point. Only the session creator can close it.', closeSessionSchema, withIdentity(closeSession));

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+{"version":3,"file":"server.js","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":";AACA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsEG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAA;AACnE,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAA;AAEhF,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,MAAM,WAAW,CAAA;AAErD,4BAA4B;AAC5B,OAAO,EAAE,WAAW,EAAE,iBAAiB,EAAE,MAAM,yBAAyB,CAAA;AACxE,OAAO,EAAE,WAAW,EAAE,iBAAiB,EAAE,MAAM,yBAAyB,CAAA;AACxE,OAAO,EACL,gBAAgB,EAChB,sBAAsB,GACvB,MAAM,+BAA+B,CAAA;AACtC,OAAO,EACL,kBAAkB,EAClB,wBAAwB,GACzB,MAAM,iCAAiC,CAAA;AACxC,OAAO,EACL,eAAe,EACf,qBAAqB,GACtB,MAAM,6BAA6B,CAAA;AAEpC,wBAAwB;AACxB,OAAO,EAAE,WAAW,EAAE,iBAAiB,EAAE,MAAM,0BAA0B,CAAA;AACzE,OAAO,EACL,kBAAkB,EAClB,wBAAwB,GACzB,MAAM,iCAAiC,CAAA;AACxC,OAAO,EAAE,UAAU,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAA;AACrE,OAAO,EACL,kBAAkB,EAClB,wBAAwB,EACxB,oBAAoB,EACpB,0BAA0B,GAC3B,MAAM,8BAA8B,CAAA;AACrC,OAAO,EACL,cAAc,EACd,oBAAoB,GACrB,MAAM,4BAA4B,CAAA;AACnC,OAAO,EACL,gBAAgB,EAChB,sBAAsB,GACvB,MAAM,8BAA8B,CAAA;AACrC,OAAO,EACL,cAAc,EACd,oBAAoB,GACrB,MAAM,4BAA4B,CAAA;AACnC,OAAO,EACL,cAAc,EACd,oBAAoB,GACrB,MAAM,4BAA4B,CAAA;AACnC,OAAO,EACL,iBAAiB,EACjB,uBAAuB,EACvB,SAAS,EACT,eAAe,EACf,UAAU,EACV,gBAAgB,GACjB,MAAM,yBAAyB,CAAA;AAChC,OAAO,EACL,YAAY,EACZ,kBAAkB,EAClB,WAAW,EACX,iBAAiB,GAClB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EACL,aAAa,EACb,mBAAmB,GACpB,MAAM,2BAA2B,CAAA;AAClC,OAAO,EAAE,SAAS,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAA;AAClE,OAAO,EACL,YAAY,EACZ,kBAAkB,EAClB,aAAa,EACb,mBAAmB,EACnB,gBAAgB,EAChB,sBAAsB,GACvB,MAAM,qBAAqB,CAAA;AAC5B,OAAO,EACL,UAAU,EACV,gBAAgB,EAChB,QAAQ,EACR,cAAc,EACd,KAAK,EACL,WAAW,EACX,MAAM,EACN,YAAY,EACZ,QAAQ,EACR,cAAc,GACf,MAAM,mBAAmB,CAAA;AAC1B,OAAO,EACL,QAAQ,EACR,cAAc,EACd,QAAQ,EACR,cAAc,EACd,UAAU,EACV,gBAAgB,GACjB,MAAM,yBAAyB,CAAA;AAChC,OAAO,EACL,MAAM,EACN,YAAY,EACZ,KAAK,EACL,WAAW,EACX,QAAQ,EACR,cAAc,EACd,QAAQ,EACR,cAAc,EACd,QAAQ,EACR,cAAc,EACd,QAAQ,EACR,cAAc,EACd,eAAe,EACf,qBAAqB,GACtB,MAAM,uBAAuB,CAAA;AAC9B,OAAO,EACL,gBAAgB,EAChB,sBAAsB,GACvB,MAAM,+BAA+B,CAAA;AAEtC,sBAAsB;AACtB,OAAO,EACL,cAAc,EACd,oBAAoB,EACpB,iBAAiB,EACjB,uBAAuB,EACvB,eAAe,EACf,qBAAqB,GACtB,MAAM,uBAAuB,CAAA;AAE9B,mBAAmB;AACnB,OAAO,EACL,SAAS,EACT,eAAe,EACf,QAAQ,EACR,cAAc,EACd,QAAQ,EACR,cAAc,EACd,KAAK,EACL,WAAW,EACX,MAAM,EACN,YAAY,GACb,MAAM,oBAAoB,CAAA;AAE3B,8EAA8E;AAC9E,4BAA4B;AAC5B,8EAA8E;AAE9E;;;GAGG;AACH,8DAA8D;AAC9D,SAAS,YAAY,CAAC,OAAoC;IACxD,8DAA8D;IAC9D,OAAO,KAAK,EAAE,IAAS,EAAE,EAAE;QACzB,MAAM,QAAQ,GAAG,WAAW,EAAE,CAAA;QAC9B,OAAO,OAAO,CAAC,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;IACvD,CAAC,CAAA;AACH,CAAC;AAED,8EAA8E;AAC9E,eAAe;AACf,8EAA8E;AAE9E,MAAM,MAAM,GAAG,IAAI,SAAS,CAC1B;IACE,IAAI,EAAE,WAAW;IACjB,OAAO,EAAE,OAAO;CACjB,EACD;IACE,YAAY,EAAE;QACZ,KAAK,EAAE,EAAE;KACV;CACF,CACF,CAAA;AAED,8EAA8E;AAC9E,kCAAkC;AAClC,8EAA8E;AAE9E,MAAM,CAAC,IAAI,CACT,WAAW,EACX,qKAAqK,EACrK,qBAAqB,EACrB,KAAK,EAAE,IAAI,EAAE,EAAE,CAAC,eAAe,CAAC,IAAI,CAAC,CACtC,CAAA;AAED,MAAM,CAAC,IAAI,CACT,WAAW,EACX,qLAAqL,EACrL,sBAAsB,EACtB,KAAK,EAAE,IAAI,EAAE,EAAE,CAAC,gBAAgB,CAAC,IAAI,CAAC,CACvC,CAAA;AAED,MAAM,CAAC,IAAI,CACT,QAAQ,EACR,sKAAsK,EACtK,iBAAiB,EACjB,KAAK,EAAE,IAAI,EAAE,EAAE,CAAC,WAAW,CAAC,IAAI,CAAC,CAClC,CAAA;AAED,MAAM,CAAC,IAAI,CACT,YAAY,EACZ,8LAA8L,EAC9L,wBAAwB,EACxB,KAAK,EAAE,IAAI,EAAE,EAAE,CAAC,kBAAkB,CAAC,IAAI,CAAC,CACzC,CAAA;AAED,MAAM,CAAC,IAAI,CACT,cAAc,EACd,yGAAyG,EACzG,iBAAiB,EACjB,KAAK,EAAE,IAAI,EAAE,EAAE,CAAC,WAAW,CAAC,IAAI,CAAC,CAClC,CAAA;AAED,8EAA8E;AAC9E,8BAA8B;AAC9B,8EAA8E;AAE9E,MAAM,CAAC,IAAI,CACT,WAAW,EACX,oHAAoH,EACpH,kBAAkB,EAClB,YAAY,CAAC,YAAY,CAAC,CAC3B,CAAA;AAED,MAAM,CAAC,IAAI,CACT,UAAU,EACV,4HAA4H,EAC5H,iBAAiB,EACjB,YAAY,CAAC,WAAW,CAAC,CAC1B,CAAA;AAED,MAAM,CAAC,IAAI,CACT,UAAU,EACV,4KAA4K,EAC5K,eAAe,EACf,YAAY,CAAC,SAAS,CAAC,CACxB,CAAA;AAED,MAAM,CAAC,IAAI,CACT,WAAW,EACX,mJAAmJ,EACnJ,gBAAgB,EAChB,YAAY,CAAC,UAAU,CAAC,CACzB,CAAA;AAED,MAAM,CAAC,IAAI,CACT,QAAQ,EACR,0IAA0I,EAC1I,uBAAuB,EACvB,YAAY,CAAC,iBAAiB,CAAC,CAChC,CAAA;AAED,MAAM,CAAC,IAAI,CACT,aAAa,EACb,oEAAoE,EACpE,gBAAgB,EAChB,YAAY,CAAC,UAAU,CAAC,CACzB,CAAA;AAED,MAAM,CAAC,IAAI,CACT,aAAa,EACb,4IAA4I,EAC5I,sBAAsB,EACtB,YAAY,CAAC,gBAAgB,CAAC,CAC/B,CAAA;AAED,MAAM,CAAC,IAAI,CACT,WAAW,EACX,2JAA2J,EAC3J,iBAAiB,EACjB,YAAY,CAAC,WAAW,CAAC,CAC1B,CAAA;AAED,MAAM,CAAC,IAAI,CACT,WAAW,EACX,iHAAiH,EACjH,eAAe,EACf,YAAY,CAAC,SAAS,CAAC,CACxB,CAAA;AAED,MAAM,CAAC,IAAI,CACT,YAAY,EACZ,+MAA+M,EAC/M,oBAAoB,EACpB,YAAY,CAAC,cAAc,CAAC,CAC7B,CAAA;AAED,MAAM,CAAC,IAAI,CACT,UAAU,EACV,kIAAkI,EAClI,mBAAmB,EACnB,YAAY,CAAC,aAAa,CAAC,CAC5B,CAAA;AAED,MAAM,CAAC,IAAI,CACT,cAAc,EACd,qJAAqJ,EACrJ,sBAAsB,EACtB,YAAY,CAAC,gBAAgB,CAAC,CAC/B,CAAA;AAED,MAAM,CAAC,IAAI,CACT,YAAY,EACZ,0JAA0J,EAC1J,oBAAoB,EACpB,YAAY,CAAC,cAAc,CAAC,CAC7B,CAAA;AAED,MAAM,CAAC,IAAI,CACT,YAAY,EACZ,mFAAmF,EACnF,oBAAoB,EACpB,YAAY,CAAC,cAAc,CAAC,CAC7B,CAAA;AAED,MAAM,CAAC,IAAI,CACT,gBAAgB,EAChB,wHAAwH,EACxH,wBAAwB,EACxB,YAAY,CAAC,kBAAkB,CAAC,CACjC,CAAA;AAED,MAAM,CAAC,IAAI,CACT,gBAAgB,EAChB,qJAAqJ,EACrJ,mBAAmB,EACnB,YAAY,CAAC,aAAa,CAAC,CAC5B,CAAA;AAED,MAAM,CAAC,IAAI,CACT,eAAe,EACf,yIAAyI,EACzI,kBAAkB,EAClB,YAAY,CAAC,YAAY,CAAC,CAC3B,CAAA;AAED,MAAM,CAAC,IAAI,CACT,cAAc,EACd,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package/dist/tools/append-session-entry.d.ts

@@ -26,6 +26,7 @@ export declare const appendSessionEntrySchema: {
     linked_entity_type: z.ZodOptional<z.ZodString>;
     linked_entity_id: z.ZodOptional<z.ZodString>;
     agent_id: z.ZodOptional<z.ZodString>;
+    metadata: z.ZodOptional<z.ZodString>;
 };
 type AppendSessionEntryArgs = {
     session_id: string;
@@ -35,6 +36,7 @@ type AppendSessionEntryArgs = {
     linked_entity_id?: string;
     user_id: string;
     agent_id?: string;
+    metadata?: string;
 };
 export declare function appendSessionEntry(args: AppendSessionEntryArgs): Promise<{
     content: {

package/dist/tools/append-session-entry.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"append-session-entry.d.ts","sourceRoot":"","sources":["../../src/tools/append-session-entry.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAA;AAGvB,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;CAgCpC,CAAA;AAED,KAAK,sBAAsB,GAAG;IAC5B,UAAU,EAAE,MAAM,CAAA;IAClB,UAAU,EAAE,MAAM,CAAA;IAClB,OAAO,EAAE,MAAM,CAAA;IACf,kBAAkB,CAAC,EAAE,MAAM,CAAA;IAC3B,gBAAgB,CAAC,EAAE,MAAM,CAAA;IACzB,OAAO,EAAE,MAAM,CAAA;IACf,QAAQ,CAAC,EAAE,MAAM,CAAA;CAClB,CAAA;AAED,wBAAsB,kBAAkB,CAAC,IAAI,EAAE,sBAAsB;;;;;;;;;;;;GA4BpE"}
+{"version":3,"file":"append-session-entry.d.ts","sourceRoot":"","sources":["../../src/tools/append-session-entry.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAA;AAGvB,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;;CAwCpC,CAAA;AAED,KAAK,sBAAsB,GAAG;IAC5B,UAAU,EAAE,MAAM,CAAA;IAClB,UAAU,EAAE,MAAM,CAAA;IAClB,OAAO,EAAE,MAAM,CAAA;IACf,kBAAkB,CAAC,EAAE,MAAM,CAAA;IAC3B,gBAAgB,CAAC,EAAE,MAAM,CAAA;IACzB,OAAO,EAAE,MAAM,CAAA;IACf,QAAQ,CAAC,EAAE,MAAM,CAAA;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAA;CAClB,CAAA;AAED,wBAAsB,kBAAkB,CAAC,IAAI,EAAE,sBAAsB;;;;;;;;;;;;GA8CpE"}

package/dist/tools/append-session-entry.js

@@ -37,8 +37,31 @@ export const appendSessionEntrySchema = {
         .optional()
         .describe('UUID of the linked entity'),
     agent_id: z.string().max(200).optional().describe('Agent identifier if applicable'),
+    metadata: z
+        .string()
+        .max(10_000)
+        .optional()
+        .describe('JSON string of metadata to merge into the session entry. ' +
+        'Example: \'{"model": "claude-opus-4", "toolstack": "opencode", "machine_id": "..."}\''),
 };
 export async function appendSessionEntry(args) {
+    let parsedMetadata;
+    if (args.metadata) {
+        try {
+            parsedMetadata = JSON.parse(args.metadata);
+        }
+        catch {
+            return {
+                content: [
+                    {
+                        type: 'text',
+                        text: JSON.stringify({ error: 'metadata must be a valid JSON string' }, null, 2),
+                    },
+                ],
+                isError: true,
+            };
+        }
+    }
     const result = await nexusPost('/api/mcp/sessions', {
         action: 'session_append',
         session_id: args.session_id,
@@ -47,6 +70,7 @@ export async function appendSessionEntry(args) {
         agent_id: args.agent_id,
         linked_entity_type: args.linked_entity_type,
         linked_entity_id: args.linked_entity_id,
+        ...(parsedMetadata ? { metadata: parsedMetadata } : {}),
     });
     if (!result.ok) {
         return {

package/dist/tools/append-session-entry.js.map

@@ -1 +1 @@
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+{"version":3,"file":"append-session-entry.js","sourceRoot":"","sources":["../../src/tools/append-session-entry.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAA;AACvB,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAE3C,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;IACnE,UAAU,EAAE,CAAC;SACV,IAAI,CAAC;QACJ,qBAAqB;QACrB,cAAc;QACd,cAAc;QACd,aAAa;QACb,gBAAgB;QAChB,gBAAgB;QAChB,mBAAmB;QACnB,aAAa;QACb,cAAc;QACd,kBAAkB;QAClB,MAAM;QACN,YAAY;KACb,CAAC;SACD,QAAQ,CAAC,uBAAuB,CAAC;IACpC,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,QAAQ,CAAC,8BAA8B,CAAC;IACzE,kBAAkB,EAAE,CAAC;SAClB,MAAM,EAAE;SACR,GAAG,CAAC,EAAE,CAAC;SACP,QAAQ,EAAE;SACV,QAAQ,CACP,6EAA6E,CAC9E;IACH,gBAAgB,EAAE,CAAC;SAChB,MAAM,EAAE;SACR,IAAI,EAAE;SACN,QAAQ,EAAE;SACV,QAAQ,CAAC,2BAA2B,CAAC;IACxC,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;IACnF,QAAQ,EAAE,CAAC;SACR,MAAM,EAAE;SACR,GAAG,CAAC,MAAM,CAAC;SACX,QAAQ,EAAE;SACV,QAAQ,CACP,2DAA2D;QACzD,uFAAuF,CAC1F;CACJ,CAAA;AAaD,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,IAA4B;IACnE,IAAI,cAAmD,CAAA;IACvD,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;QAClB,IAAI,CAAC;YACH,cAAc,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QAC5C,CAAC;QAAC,MAAM,CAAC;YACP,OAAO;gBACL,OAAO,EAAE;oBACP;wBACE,IAAI,EAAE,MAAe;wBACrB,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,sCAAsC,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC;qBACjF;iBACF;gBACD,OAAO,EAAE,IAAI;aACd,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,mBAAmB,EAAE;QAClD,MAAM,EAAE,gBAAgB;QACxB,UAAU,EAAE,IAAI,CAAC,UAAU;QAC3B,UAAU,EAAE,IAAI,CAAC,UAAU;QAC3B,OAAO,EAAE,IAAI,CAAC,OAAO;QACrB,QAAQ,EAAE,IAAI,CAAC,QAAQ;QACvB,kBAAkB,EAAE,IAAI,CAAC,kBAAkB;QAC3C,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;QACvC,GAAG,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,cAAc,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;KACxD,CAAC,CAAA;IAEF,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;QACf,OAAO;YACL,OAAO,EAAE;gBACP;oBACE,IAAI,EAAE,MAAe;oBACrB,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC;iBACvD;aACF;YACD,OAAO,EAAE,IAAI;SACd,CAAA;IACH,CAAC;IAED,OAAO;QACL,OAAO,EAAE;YACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,EAAE;SACtE;KACF,CAAA;AACH,CAAC"}

package/dist/tools/classify-document.d.ts

@@ -0,0 +1,38 @@
+/**
+ * doc_classify -- Layer 2 Coordination
+ *
+ * Update the classification of an ingest item.
+ * Delegates to POST /api/mcp/documents (action: doc_classify).
+ */
+import { z } from 'zod';
+export declare const classifyDocumentSchema: {
+    document_id: z.ZodString;
+    classification: z.ZodEnum<{
+        research_note: "research_note";
+        planning_item: "planning_item";
+        unclassified: "unclassified";
+        decision_input: "decision_input";
+        reference: "reference";
+        archive: "archive";
+    }>;
+};
+type ClassifyDocumentArgs = {
+    document_id: string;
+    classification: string;
+    user_id: string;
+};
+export declare function classifyDocument(args: ClassifyDocumentArgs): Promise<{
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    isError: boolean;
+} | {
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    isError?: undefined;
+}>;
+export {};
+//# sourceMappingURL=classify-document.d.ts.map

package/dist/tools/classify-document.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"classify-document.d.ts","sourceRoot":"","sources":["../../src/tools/classify-document.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAA;AAGvB,eAAO,MAAM,sBAAsB;;;;;;;;;;CAYlC,CAAA;AAED,KAAK,oBAAoB,GAAG;IAC1B,WAAW,EAAE,MAAM,CAAA;IACnB,cAAc,EAAE,MAAM,CAAA;IACtB,OAAO,EAAE,MAAM,CAAA;CAChB,CAAA;AAED,wBAAsB,gBAAgB,CAAC,IAAI,EAAE,oBAAoB;;;;;;;;;;;;GAwBhE"}

package/dist/tools/classify-document.js

@@ -0,0 +1,45 @@
+/**
+ * doc_classify -- Layer 2 Coordination
+ *
+ * Update the classification of an ingest item.
+ * Delegates to POST /api/mcp/documents (action: doc_classify).
+ */
+import { z } from 'zod';
+import { nexusPost } from '../nexus-api.js';
+export const classifyDocumentSchema = {
+    document_id: z.string().uuid().describe('Document UUID to classify'),
+    classification: z
+        .enum([
+        'unclassified',
+        'research_note',
+        'planning_item',
+        'decision_input',
+        'reference',
+        'archive',
+    ])
+        .describe('New classification for the document'),
+};
+export async function classifyDocument(args) {
+    const result = await nexusPost('/api/mcp/documents', {
+        action: 'doc_classify',
+        document_id: args.document_id,
+        classification: args.classification,
+    });
+    if (!result.ok) {
+        return {
+            content: [
+                {
+                    type: 'text',
+                    text: JSON.stringify({ error: result.error }, null, 2),
+                },
+            ],
+            isError: true,
+        };
+    }
+    return {
+        content: [
+            { type: 'text', text: JSON.stringify(result.data, null, 2) },
+        ],
+    };
+}
+//# sourceMappingURL=classify-document.js.map

package/dist/tools/classify-document.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"classify-document.js","sourceRoot":"","sources":["../../src/tools/classify-document.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAA;AACvB,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAE3C,MAAM,CAAC,MAAM,sBAAsB,GAAG;IACpC,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;IACpE,cAAc,EAAE,CAAC;SACd,IAAI,CAAC;QACJ,cAAc;QACd,eAAe;QACf,eAAe;QACf,gBAAgB;QAChB,WAAW;QACX,SAAS;KACV,CAAC;SACD,QAAQ,CAAC,qCAAqC,CAAC;CACnD,CAAA;AAQD,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,IAA0B;IAC/D,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,oBAAoB,EAAE;QACnD,MAAM,EAAE,cAAc;QACtB,WAAW,EAAE,IAAI,CAAC,WAAW;QAC7B,cAAc,EAAE,IAAI,CAAC,cAAc;KACpC,CAAC,CAAA;IAEF,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;QACf,OAAO;YACL,OAAO,EAAE;gBACP;oBACE,IAAI,EAAE,MAAe;oBACrB,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC;iBACvD;aACF;YACD,OAAO,EAAE,IAAI;SACd,CAAA;IACH,CAAC;IAED,OAAO;QACL,OAAO,EAAE;YACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,EAAE;SACtE;KACF,CAAA;AACH,CAAC"}

package/dist/tools/delete-document.d.ts

@@ -0,0 +1,29 @@
+/**
+ * doc_delete -- Layer 2 Coordination
+ *
+ * Delete an ingest item from a project's knowledge base.
+ * Delegates to POST /api/mcp/documents (action: doc_delete).
+ */
+import { z } from 'zod';
+export declare const deleteDocumentSchema: {
+    document_id: z.ZodString;
+};
+type DeleteDocumentArgs = {
+    document_id: string;
+    user_id: string;
+};
+export declare function deleteDocument(args: DeleteDocumentArgs): Promise<{
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    isError: boolean;
+} | {
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    isError?: undefined;
+}>;
+export {};
+//# sourceMappingURL=delete-document.d.ts.map

package/dist/tools/delete-document.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"delete-document.d.ts","sourceRoot":"","sources":["../../src/tools/delete-document.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAA;AAGvB,eAAO,MAAM,oBAAoB;;CAEhC,CAAA;AAED,KAAK,kBAAkB,GAAG;IACxB,WAAW,EAAE,MAAM,CAAA;IACnB,OAAO,EAAE,MAAM,CAAA;CAChB,CAAA;AAED,wBAAsB,cAAc,CAAC,IAAI,EAAE,kBAAkB;;;;;;;;;;;;GAuB5D"}

package/dist/tools/delete-document.js

@@ -0,0 +1,34 @@
+/**
+ * doc_delete -- Layer 2 Coordination
+ *
+ * Delete an ingest item from a project's knowledge base.
+ * Delegates to POST /api/mcp/documents (action: doc_delete).
+ */
+import { z } from 'zod';
+import { nexusPost } from '../nexus-api.js';
+export const deleteDocumentSchema = {
+    document_id: z.string().uuid().describe('Document UUID to delete'),
+};
+export async function deleteDocument(args) {
+    const result = await nexusPost('/api/mcp/documents', {
+        action: 'doc_delete',
+        document_id: args.document_id,
+    });
+    if (!result.ok) {
+        return {
+            content: [
+                {
+                    type: 'text',
+                    text: JSON.stringify({ error: result.error }, null, 2),
+                },
+            ],
+            isError: true,
+        };
+    }
+    return {
+        content: [
+            { type: 'text', text: JSON.stringify(result.data, null, 2) },
+        ],
+    };
+}
+//# sourceMappingURL=delete-document.js.map

package/dist/tools/delete-document.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"delete-document.js","sourceRoot":"","sources":["../../src/tools/delete-document.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAA;AACvB,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAE3C,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;CACnE,CAAA;AAOD,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,IAAwB;IAC3D,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,oBAAoB,EAAE;QACnD,MAAM,EAAE,YAAY;QACpB,WAAW,EAAE,IAAI,CAAC,WAAW;KAC9B,CAAC,CAAA;IAEF,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;QACf,OAAO;YACL,OAAO,EAAE;gBACP;oBACE,IAAI,EAAE,MAAe;oBACrB,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC;iBACvD;aACF;YACD,OAAO,EAAE,IAAI;SACd,CAAA;IACH,CAAC;IAED,OAAO;QACL,OAAO,EAAE;YACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,EAAE;SACtE;KACF,CAAA;AACH,CAAC"}

package/dist/tools/reviews.d.ts

@@ -86,11 +86,11 @@ export declare const rvDecideSchema: {
     review_id: z.ZodString;
     transition: z.ZodEnum<{
         accept: "accept";
+        archive: "archive";
         submit: "submit";
         reject: "reject";
         request_revision: "request_revision";
         resubmit: "resubmit";
-        archive: "archive";
     }>;
     rationale: z.ZodOptional<z.ZodString>;
 };

package/dist/tools/update-document.d.ts

@@ -0,0 +1,38 @@
+/**
+ * doc_update -- Layer 2 Coordination
+ *
+ * Update title, body, or source_url of an ingest item.
+ * Supports full body replacement or append mode.
+ * Delegates to POST /api/mcp/documents (action: doc_update).
+ */
+import { z } from 'zod';
+export declare const updateDocumentSchema: {
+    document_id: z.ZodString;
+    title: z.ZodOptional<z.ZodString>;
+    body: z.ZodOptional<z.ZodString>;
+    source_url: z.ZodOptional<z.ZodString>;
+    append_body: z.ZodOptional<z.ZodString>;
+};
+type UpdateDocumentArgs = {
+    document_id: string;
+    title?: string;
+    body?: string;
+    source_url?: string;
+    append_body?: string;
+    user_id: string;
+};
+export declare function updateDocument(args: UpdateDocumentArgs): Promise<{
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    isError: boolean;
+} | {
+    content: {
+        type: "text";
+        text: string;
+    }[];
+    isError?: undefined;
+}>;
+export {};
+//# sourceMappingURL=update-document.d.ts.map

package/dist/tools/update-document.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"update-document.d.ts","sourceRoot":"","sources":["../../src/tools/update-document.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAA;AAGvB,eAAO,MAAM,oBAAoB;;;;;;CAgBhC,CAAA;AAED,KAAK,kBAAkB,GAAG;IACxB,WAAW,EAAE,MAAM,CAAA;IACnB,KAAK,CAAC,EAAE,MAAM,CAAA;IACd,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,UAAU,CAAC,EAAE,MAAM,CAAA;IACnB,WAAW,CAAC,EAAE,MAAM,CAAA;IACpB,OAAO,EAAE,MAAM,CAAA;CAChB,CAAA;AAED,wBAAsB,cAAc,CAAC,IAAI,EAAE,kBAAkB;;;;;;;;;;;;GA2B5D"}

package/dist/tools/update-document.js

@@ -0,0 +1,51 @@
+/**
+ * doc_update -- Layer 2 Coordination
+ *
+ * Update title, body, or source_url of an ingest item.
+ * Supports full body replacement or append mode.
+ * Delegates to POST /api/mcp/documents (action: doc_update).
+ */
+import { z } from 'zod';
+import { nexusPost } from '../nexus-api.js';
+export const updateDocumentSchema = {
+    document_id: z.string().uuid().describe('Document UUID to update'),
+    title: z.string().max(500).optional().describe('New document title'),
+    body: z
+        .string()
+        .max(100_000)
+        .optional()
+        .describe('New document body (replaces existing content)'),
+    source_url: z.string().url().optional().describe('Updated source URL'),
+    append_body: z
+        .string()
+        .max(100_000)
+        .optional()
+        .describe('Content to append to existing body (ignored if body is also provided)'),
+};
+export async function updateDocument(args) {
+    const result = await nexusPost('/api/mcp/documents', {
+        action: 'doc_update',
+        document_id: args.document_id,
+        title: args.title,
+        body: args.body,
+        source_url: args.source_url,
+        append_body: args.append_body,
+    });
+    if (!result.ok) {
+        return {
+            content: [
+                {
+                    type: 'text',
+                    text: JSON.stringify({ error: result.error }, null, 2),
+                },
+            ],
+            isError: true,
+        };
+    }
+    return {
+        content: [
+            { type: 'text', text: JSON.stringify(result.data, null, 2) },
+        ],
+    };
+}
+//# sourceMappingURL=update-document.js.map

package/dist/tools/update-document.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"update-document.js","sourceRoot":"","sources":["../../src/tools/update-document.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAA;AACvB,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAE3C,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;IAClE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;IACpE,IAAI,EAAE,CAAC;SACJ,MAAM,EAAE;SACR,GAAG,CAAC,OAAO,CAAC;SACZ,QAAQ,EAAE;SACV,QAAQ,CAAC,+CAA+C,CAAC;IAC5D,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;IACtE,WAAW,EAAE,CAAC;SACX,MAAM,EAAE;SACR,GAAG,CAAC,OAAO,CAAC;SACZ,QAAQ,EAAE;SACV,QAAQ,CACP,uEAAuE,CACxE;CACJ,CAAA;AAWD,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,IAAwB;IAC3D,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,oBAAoB,EAAE;QACnD,MAAM,EAAE,YAAY;QACpB,WAAW,EAAE,IAAI,CAAC,WAAW;QAC7B,KAAK,EAAE,IAAI,CAAC,KAAK;QACjB,IAAI,EAAE,IAAI,CAAC,IAAI;QACf,UAAU,EAAE,IAAI,CAAC,UAAU;QAC3B,WAAW,EAAE,IAAI,CAAC,WAAW;KAC9B,CAAC,CAAA;IAEF,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;QACf,OAAO;YACL,OAAO,EAAE;gBACP;oBACE,IAAI,EAAE,MAAe;oBACrB,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC;iBACvD;aACF;YACD,OAAO,EAAE,IAAI;SACd,CAAA;IACH,CAAC;IAED,OAAO;QACL,OAAO,EAAE;YACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,EAAE;SACtE;KACF,CAAA;AACH,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gwdn/nexus-mcp",
-  "version": "0.8.0",
+  "version": "0.8.3",
   "description": "MCP server for the Nexus platform",
   "type": "module",
   "main": "dist/server.js",

package/src/__tests__/layer2-coordination.test.ts

@@ -206,6 +206,82 @@ describe('Layer 2: session_append', () => {
 
     expect(result.isError).toBe(true)
   })
+
+  it('should forward parsed metadata to the API', async () => {
+    vi.mocked(nexusPost).mockResolvedValue(
+      mockApiSuccess({
+        action: 'session_append',
+        entry_id: TEST_IDS.entryId,
+        session_id: TEST_IDS.sessionId,
+        entry_type: 'note',
+        project_id: TEST_IDS.projectId,
+      }),
+    )
+
+    const { appendSessionEntry } = await import('../tools/append-session-entry.js')
+    const metadata = JSON.stringify({
+      model: 'claude-opus-4',
+      toolstack: 'opencode',
+      machine_id: '00000000-0000-0000-0000-000000000001',
+    })
+    const result = await appendSessionEntry({
+      session_id: TEST_IDS.sessionId,
+      entry_type: 'note',
+      summary: 'Entry with metadata',
+      user_id: TEST_IDS.userId,
+      metadata,
+    })
+
+    expect(result.isError).toBeUndefined()
+    expect(vi.mocked(nexusPost)).toHaveBeenCalledWith(
+      '/api/mcp/sessions',
+      expect.objectContaining({
+        metadata: {
+          model: 'claude-opus-4',
+          toolstack: 'opencode',
+          machine_id: '00000000-0000-0000-0000-000000000001',
+        },
+      }),
+    )
+  })
+
+  it('should return error for invalid metadata JSON', async () => {
+    const { appendSessionEntry } = await import('../tools/append-session-entry.js')
+    const result = await appendSessionEntry({
+      session_id: TEST_IDS.sessionId,
+      entry_type: 'note',
+      summary: 'Bad metadata',
+      user_id: TEST_IDS.userId,
+      metadata: '{invalid json',
+    })
+
+    expect(result.isError).toBe(true)
+    const parsed = parseToolResponse(result)
+    expect(parsed.error).toContain('valid JSON')
+  })
+
+  it('should omit metadata key when not provided', async () => {
+    vi.mocked(nexusPost).mockResolvedValue(
+      mockApiSuccess({
+        action: 'session_append',
+        entry_id: TEST_IDS.entryId,
+        session_id: TEST_IDS.sessionId,
+        entry_type: 'note',
+        project_id: TEST_IDS.projectId,
+      }),
+    )
+
+    const { appendSessionEntry } = await import('../tools/append-session-entry.js')
+    await appendSessionEntry({
+      session_id: TEST_IDS.sessionId,
+      entry_type: 'note',
+      summary: 'No metadata',
+      user_id: TEST_IDS.userId,
+    })
+
+    const call = vi.mocked(nexusPost).mock.calls[0][1] as Record<string, unknown>
+    expect(call).not.toHaveProperty('metadata')
+  })
 })
 
 // ---------------------------------------------------------------------------

package/src/__tests__/server.test.ts

@@ -78,9 +78,9 @@ describe('MCP Server: withIdentity wrapper', () => {
 })
 
 describe('MCP Server: Schema exports', () => {
-  const EXPECTED_TOOL_COUNT = 45
+  const EXPECTED_TOOL_COUNT = 48
 
-  it('should register exactly 45 tools in server.ts', () => {
+  it('should register exactly 48 tools in server.ts', () => {
     // Static analysis: count server.tool( calls in server.ts as a regression guard.
     // If you add or remove a tool, update EXPECTED_TOOL_COUNT above.
     const serverSource = readFileSync(
@@ -146,6 +146,7 @@ describe('MCP Server: Schema exports', () => {
 
     const appendEntry = await import('../tools/append-session-entry.js')
     expect(appendEntry.appendSessionEntrySchema).toBeDefined()
+    expect(appendEntry.appendSessionEntrySchema.metadata).toBeDefined()
     expect(typeof appendEntry.appendSessionEntry).toBe('function')
 
     const letters = await import('../tools/letters.js')

package/src/server.ts

@@ -109,6 +109,18 @@ import {
   ingestDocument,
   ingestDocumentSchema,
 } from './tools/ingest-document.js'
+import {
+  classifyDocument,
+  classifyDocumentSchema,
+} from './tools/classify-document.js'
+import {
+  updateDocument,
+  updateDocumentSchema,
+} from './tools/update-document.js'
+import {
+  deleteDocument,
+  deleteDocumentSchema,
+} from './tools/delete-document.js'
 import {
   acknowledgeLetter,
   acknowledgeLetterSchema,
@@ -354,6 +366,27 @@ server.tool(
   withIdentity(listDocuments),
 )
 
+server.tool(
+  'doc_classify',
+  'Update the classification of an ingest item. Valid classifications: unclassified, research_note, planning_item, decision_input, reference, archive.',
+  classifyDocumentSchema,
+  withIdentity(classifyDocument),
+)
+
+server.tool(
+  'doc_update',
+  'Update title, body, or source_url of an ingest item. Supports full body replacement or append mode via append_body. At least one field must be provided.',
+  updateDocumentSchema,
+  withIdentity(updateDocument),
+)
+
+server.tool(
+  'doc_delete',
+  'Delete an ingest item from a project knowledge base. This action is irreversible.',
+  deleteDocumentSchema,
+  withIdentity(deleteDocument),
+)
+
 server.tool(
   'session_append',
   'Append an entry to an existing session. Enforces session write isolation: only the session creator can append entries.',

package/src/tools/append-session-entry.ts

@@ -41,6 +41,14 @@ export const appendSessionEntrySchema = {
     .optional()
     .describe('UUID of the linked entity'),
   agent_id: z.string().max(200).optional().describe('Agent identifier if applicable'),
+  metadata: z
+    .string()
+    .max(10_000)
+    .optional()
+    .describe(
+      'JSON string of metadata to merge into the session entry. ' +
+        'Example: \'{"model": "claude-opus-4", "toolstack": "opencode", "machine_id": "..."}\'',
+    ),
 }
 
 type AppendSessionEntryArgs = {
@@ -51,9 +59,27 @@ type AppendSessionEntryArgs = {
   linked_entity_id?: string
   user_id: string
   agent_id?: string
+  metadata?: string
 }
 
 export async function appendSessionEntry(args: AppendSessionEntryArgs) {
+  let parsedMetadata: Record<string, unknown> | undefined
+  if (args.metadata) {
+    try {
+      parsedMetadata = JSON.parse(args.metadata)
+    } catch {
+      return {
+        content: [
+          {
+            type: 'text' as const,
+            text: JSON.stringify({ error: 'metadata must be a valid JSON string' }, null, 2),
+          },
+        ],
+        isError: true,
+      }
+    }
+  }
+
   const result = await nexusPost('/api/mcp/sessions', {
     action: 'session_append',
     session_id: args.session_id,
@@ -62,6 +88,7 @@ export async function appendSessionEntry(args: AppendSessionEntryArgs) {
     agent_id: args.agent_id,
     linked_entity_type: args.linked_entity_type,
     linked_entity_id: args.linked_entity_id,
+    ...(parsedMetadata ? { metadata: parsedMetadata } : {}),
   })
 
   if (!result.ok) {

package/src/tools/classify-document.ts

@@ -0,0 +1,55 @@
+/**
+ * doc_classify -- Layer 2 Coordination
+ *
+ * Update the classification of an ingest item.
+ * Delegates to POST /api/mcp/documents (action: doc_classify).
+ */
+
+import { z } from 'zod'
+import { nexusPost } from '../nexus-api.js'
+
+export const classifyDocumentSchema = {
+  document_id: z.string().uuid().describe('Document UUID to classify'),
+  classification: z
+    .enum([
+      'unclassified',
+      'research_note',
+      'planning_item',
+      'decision_input',
+      'reference',
+      'archive',
+    ])
+    .describe('New classification for the document'),
+}
+
+type ClassifyDocumentArgs = {
+  document_id: string
+  classification: string
+  user_id: string
+}
+
+export async function classifyDocument(args: ClassifyDocumentArgs) {
+  const result = await nexusPost('/api/mcp/documents', {
+    action: 'doc_classify',
+    document_id: args.document_id,
+    classification: args.classification,
+  })
+
+  if (!result.ok) {
+    return {
+      content: [
+        {
+          type: 'text' as const,
+          text: JSON.stringify({ error: result.error }, null, 2),
+        },
+      ],
+      isError: true,
+    }
+  }
+
+  return {
+    content: [
+      { type: 'text' as const, text: JSON.stringify(result.data, null, 2) },
+    ],
+  }
+}

package/src/tools/delete-document.ts

@@ -0,0 +1,43 @@
+/**
+ * doc_delete -- Layer 2 Coordination
+ *
+ * Delete an ingest item from a project's knowledge base.
+ * Delegates to POST /api/mcp/documents (action: doc_delete).
+ */
+
+import { z } from 'zod'
+import { nexusPost } from '../nexus-api.js'
+
+export const deleteDocumentSchema = {
+  document_id: z.string().uuid().describe('Document UUID to delete'),
+}
+
+type DeleteDocumentArgs = {
+  document_id: string
+  user_id: string
+}
+
+export async function deleteDocument(args: DeleteDocumentArgs) {
+  const result = await nexusPost('/api/mcp/documents', {
+    action: 'doc_delete',
+    document_id: args.document_id,
+  })
+
+  if (!result.ok) {
+    return {
+      content: [
+        {
+          type: 'text' as const,
+          text: JSON.stringify({ error: result.error }, null, 2),
+        },
+      ],
+      isError: true,
+    }
+  }
+
+  return {
+    content: [
+      { type: 'text' as const, text: JSON.stringify(result.data, null, 2) },
+    ],
+  }
+}

package/src/tools/update-document.ts

@@ -0,0 +1,66 @@
+/**
+ * doc_update -- Layer 2 Coordination
+ *
+ * Update title, body, or source_url of an ingest item.
+ * Supports full body replacement or append mode.
+ * Delegates to POST /api/mcp/documents (action: doc_update).
+ */
+
+import { z } from 'zod'
+import { nexusPost } from '../nexus-api.js'
+
+export const updateDocumentSchema = {
+  document_id: z.string().uuid().describe('Document UUID to update'),
+  title: z.string().max(500).optional().describe('New document title'),
+  body: z
+    .string()
+    .max(100_000)
+    .optional()
+    .describe('New document body (replaces existing content)'),
+  source_url: z.string().url().optional().describe('Updated source URL'),
+  append_body: z
+    .string()
+    .max(100_000)
+    .optional()
+    .describe(
+      'Content to append to existing body (ignored if body is also provided)',
+    ),
+}
+
+type UpdateDocumentArgs = {
+  document_id: string
+  title?: string
+  body?: string
+  source_url?: string
+  append_body?: string
+  user_id: string
+}
+
+export async function updateDocument(args: UpdateDocumentArgs) {
+  const result = await nexusPost('/api/mcp/documents', {
+    action: 'doc_update',
+    document_id: args.document_id,
+    title: args.title,
+    body: args.body,
+    source_url: args.source_url,
+    append_body: args.append_body,
+  })
+
+  if (!result.ok) {
+    return {
+      content: [
+        {
+          type: 'text' as const,
+          text: JSON.stringify({ error: result.error }, null, 2),
+        },
+      ],
+      isError: true,
+    }
+  }
+
+  return {
+    content: [
+      { type: 'text' as const, text: JSON.stringify(result.data, null, 2) },
+    ],
+  }
+}