nexus-canon 1.0.0 → 1.2.0

package/README.md

@@ -8,7 +8,10 @@ provider, and any harness. This package is the standalone pipeline: scaffold a
 store, sync native harness session files into it, maintain the canonical line,
 and pull sessions back out wherever you want to resume. Capability artifacts
 (skills, agents, MCP configs) and project-scoped knowledge graphs ride the same
-store.
+store — graphs join the history and code halves in one NetworkX node-link file:
+session→file `touched` edges scanned from tool-call content, plus an
+auto-detected [graphify](https://github.com/Graphify-Labs/graphify) code graph
+when present, every edge confidence-tagged.
 
 ```bash
 npm i -g nexus-canon

package/dist/canonGraph.d.ts

@@ -7,7 +7,11 @@ export interface ProjectEntry {
     sessionPaths: Record<string, string[]>;
     sessionCounts: Record<string, number>;
 }
-/** Derive the authoritative project ↔ session-path map from store paths. */
+/**
+ * Derive the authoritative project ↔ session-path map from store paths.
+ * Fully environment-derived ($HOME + filesystem + the store's own dirs);
+ * `projects/ROOTS.json` overrides win where present. No hardcoded roots.
+ */
 export declare function deriveProjectSessionMap(store: string): Record<string, ProjectEntry>;
 /** Resolve which project a canon session belongs to (by path prefix). */
 export declare function sessionProject(projects: Record<string, ProjectEntry>, s: CanonSession): string | undefined;
@@ -17,6 +21,8 @@ export interface CanonGraphOptions {
     project?: string;
     /** Path to an external (graphify) node-link graph.json to fold into each project graph. */
     mergeGraph?: string;
+    /** Scan session content for session→file `touched` edges (default true; cached, incremental). */
+    touched?: boolean;
     dryRun?: boolean;
 }
 export interface CanonGraphResult {

package/dist/canonGraph.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"canonGraph.d.ts","sourceRoot":"","sources":["../src/canonGraph.ts"],"names":[],"mappings":"AAgCA,OAAO,EAAyB,KAAK,YAAY,EAAE,MAAM,gBAAgB,CAAC;AAK1E,MAAM,WAAW,YAAY;IAC3B,EAAE,EAAE,MAAM,CAAC;IACX,0GAA0G;IAC1G,IAAI,EAAE,MAAM,CAAC;IACb,6DAA6D;IAC7D,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC;IACvC,aAAa,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CACvC;AAwCD;;;;GAIG;AACH,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE,YAAY,CAAC,CAkDnF;AAED,yEAAyE;AACzE,wBAAgB,cAAc,CAAC,QAAQ,EAAE,MAAM,CAAC,MAAM,EAAE,YAAY,CAAC,EAAE,CAAC,EAAE,YAAY,GAAG,MAAM,GAAG,SAAS,CAO1G;AAED,MAAM,WAAW,iBAAiB;IAChC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,8DAA8D;IAC9D,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,2FAA2F;IAC3F,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,iGAAiG;IACjG,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,gBAAgB;IAC/B,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,OAAO,CAAC;CACjB;AAED,mGAAmG;AACnG,wBAAsB,UAAU,CAAC,CAAC,GAAE,iBAAsB,GAAG,OAAO,CAAC,gBAAgB,CAAC,CAuOrF"}

package/dist/canonGraph.js

@@ -31,29 +31,63 @@ import * as fs from 'node:fs';
 import * as path from 'node:path';
 import { execFileSync } from 'node:child_process';
 import { discoverCanonSessions } from './canonPull.js';
+import { buildTouchedIndex } from './canonTouched.js';
 const CONFIDENCE_SCORE = { EXTRACTED: 1.0, INFERRED: 0.5, AMBIGUOUS: 0.2 };
-/** Known roots: exact encoded-form matches. Everything else derives its own entry. */
-const KNOWN_ROOTS = [
-    ['workspace', '/home/runner/workspace'],
-    ['omniclaude-v4', '/home/runner/workspace/omniclaude-v4'],
-    ['nexus-terminal', '/home/runner/workspace/nexus-terminal'],
-];
 const encodeCC = (root) => root.replace(/[/.]/g, '-');
-/** cortex label → project id (labels that are sub-roots of a project). */
-const CORTEX_LABEL_PROJECT = {
-    workspace: 'workspace', 'omniclaude-v4': 'omniclaude-v4', server: 'omniclaude-v4', 'nexus-terminal': 'nexus-terminal',
-};
-/** Derive the authoritative project ↔ session-path map from store paths. */
+/**
+ * Decode a Claude-Code-encoded path remainder against the real filesystem.
+ * The encoding maps both `/` and `.` to `-`, so it is lossy; we DFS the
+ * segment joins ('-'-in-name vs '/'-descend) preferring paths that exist.
+ * Falls back to `<base>/<remainder-verbatim>` (unverified) when nothing
+ * matches — e.g. a store cloned on a machine that never held the code.
+ */
+function fsResolveEncoded(base, remainder) {
+    const segs = remainder.split('-');
+    let best;
+    const walk = (dir, i, budget) => {
+        if (best || budget.n-- <= 0)
+            return;
+        if (i >= segs.length) {
+            if (fs.existsSync(dir))
+                best = dir;
+            return;
+        }
+        // Greedily extend the current path component before descending.
+        for (let j = segs.length; j > i; j--) {
+            const component = segs.slice(i, j).join('-');
+            const candidate = path.join(dir, component);
+            if (fs.existsSync(candidate)) {
+                walk(candidate, j, budget);
+                if (best)
+                    return;
+            }
+        }
+    };
+    walk(base, 0, { n: 256 });
+    return best ? { root: best, verified: true } : { root: path.join(base, remainder), verified: false };
+}
+/**
+ * Derive the authoritative project ↔ session-path map from store paths.
+ * Fully environment-derived ($HOME + filesystem + the store's own dirs);
+ * `projects/ROOTS.json` overrides win where present. No hardcoded roots.
+ */
 export function deriveProjectSessionMap(store) {
+    const HOME = process.env.HOME ?? process.env.USERPROFILE ?? '';
+    let cfg = {};
+    try {
+        cfg = JSON.parse(fs.readFileSync(path.join(store, 'projects', 'ROOTS.json'), 'utf8'));
+    }
+    catch { /* optional */ }
     const projects = {};
     const entry = (id, root) => (projects[id] ??= { id, root, sessionPaths: {}, sessionCounts: {} });
     const add = (id, root, harness, rel) => {
         const e = entry(id, root);
+        if (!e.root && root)
+            e.root = root;
         (e.sessionPaths[harness] ??= []).push(rel);
         e.sessionCounts[harness] = (e.sessionCounts[harness] ?? 0) + 0; // counts filled from sessions below
     };
-    const ccByEncoding = new Map(KNOWN_ROOTS.map(([id, root]) => [encodeCC(root), { id, root }]));
-    const wsPrefix = encodeCC('/home/runner/workspace') + '-';
+    const homeEnc = HOME ? encodeCC(HOME) : '';
     const ccRoot = path.join(store, 'canon', 'claude-code');
     let ccDirs = [];
     try {
@@ -61,16 +95,30 @@ export function deriveProjectSessionMap(store) {
     }
     catch { /* none */ }
     for (const dir of ccDirs.sort()) {
-        const known = ccByEncoding.get(dir);
-        if (known)
-            add(known.id, known.root, 'claude-code', path.join('claude-code', dir));
-        else if (dir.startsWith(wsPrefix)) {
-            // Unknown root — surfaces as its OWN project (blind-spot closure).
-            const id = dir.slice(wsPrefix.length);
-            add(id, `/home/runner/workspace/${id}` /* best-effort decode */, 'claude-code', path.join('claude-code', dir));
+        const rel = path.join('claude-code', dir);
+        const overrideId = cfg.claudeDirs?.[dir];
+        if (overrideId) {
+            add(overrideId, cfg.roots?.[overrideId] ?? '', 'claude-code', rel);
+            continue;
         }
-        else
-            add(dir, dir, 'claude-code', path.join('claude-code', dir));
+        if (homeEnc && dir === homeEnc) {
+            add(path.basename(HOME), HOME, 'claude-code', rel);
+            continue;
+        }
+        if (homeEnc && dir.startsWith(homeEnc + '-')) {
+            const remainder = dir.slice(homeEnc.length + 1);
+            const { root, verified } = fsResolveEncoded(HOME, remainder);
+            // Prefer the resolved basename as the id; keep the raw remainder when
+            // the basename is already claimed by a different root (collision).
+            let id = verified ? path.basename(root) : remainder;
+            if (projects[id] && projects[id].root && projects[id].root !== root)
+                id = remainder;
+            add(id, cfg.roots?.[id] ?? root, 'claude-code', rel);
+            continue;
+        }
+        // Foreign-machine or unrecognized encoding: its own project, no local root
+        // (sessions still list/graph; touched/auto-detect need a root override).
+        add(dir, cfg.roots?.[dir] ?? '', 'claude-code', rel);
     }
     const cxRoot = path.join(store, 'canon', 'nexus-cortex');
     let cxDirs = [];
@@ -79,9 +127,11 @@ export function deriveProjectSessionMap(store) {
     }
     catch { /* none */ }
     for (const label of cxDirs.sort()) {
-        const id = CORTEX_LABEL_PROJECT[label] ?? label;
-        const root = projects[id]?.root ?? KNOWN_ROOTS.find(([k]) => k === id)?.[1] ?? label;
-        add(id, root, 'nexus-cortex', path.join('nexus-cortex', label));
+        const id = cfg.cortexLabels?.[label] ?? label;
+        const existing = projects[id]?.root;
+        const guess = HOME && label === path.basename(HOME) ? HOME
+            : HOME && fs.existsSync(path.join(HOME, label)) ? path.join(HOME, label) : '';
+        add(id, existing ?? cfg.roots?.[id] ?? guess, 'nexus-cortex', path.join('nexus-cortex', label));
     }
     return projects;
 }
@@ -99,6 +149,12 @@ export function sessionProject(projects, s) {
 export async function canonGraph(o = {}) {
     const STORE = o.store ?? '/tmp/canon-store';
     const env = { ...process.env, GIT_TERMINAL_PROMPT: '0' };
+    // Auto-clone like every other verb — /tmp stores are disposable by design.
+    if (!fs.existsSync(path.join(STORE, '.git'))) {
+        const repo = process.env.CANON_REPO ?? 'https://github.com/Spitfire-Products/nexus-canon-store';
+        console.log(`[canon-graph] no store at ${STORE} — cloning ${repo}`);
+        execFileSync('git', ['clone', '-q', repo, STORE], { encoding: 'utf8', env });
+    }
     const projects = deriveProjectSessionMap(STORE);
     const sessions = discoverCanonSessions(STORE);
     for (const s of sessions) {
@@ -136,8 +192,30 @@ export async function canonGraph(o = {}) {
     }
     catch { /* untracked */ }
     const wanted = o.project ? [o.project] : Object.keys(projects).sort();
-    let totalNodes = 0, totalLinks = 0;
+    let totalNodes = 0, totalLinks = 0, unchangedGraphs = 0;
     const built = [];
+    // Session-content scan (touched edges) — streamed once per changed session,
+    // cache-served afterwards. Scans ALL mapped sessions (not just the wanted
+    // projects'): cross-project touches route to the OWNING project's graph, so
+    // a foreign session's edges into a wanted project must be discoverable.
+    let touchedIdx;
+    if (o.touched !== false) {
+        const mapped = sessions.filter((s) => sessionProject(projects, s) !== undefined);
+        touchedIdx = await buildTouchedIndex(mapped);
+        console.log(`[canon-graph] touched scan: ${touchedIdx.scanned} session(s) scanned, ${touchedIdx.cached} from cache`);
+    }
+    // Touched paths are assigned to their MOST SPECIFIC project root (roots nest:
+    // the workspace root contains the others — longest-match, never first-match).
+    const rootsByLength = Object.values(projects)
+        .filter((p) => p.root) // rootless projects (foreign-machine dirs w/o override) own no paths
+        .map((p) => ({ pid: p.id, prefix: (p.root.endsWith(path.sep) ? p.root : p.root + path.sep) }))
+        .sort((a, b) => b.prefix.length - a.prefix.length);
+    const ownerOf = (abs) => {
+        for (const r of rootsByLength)
+            if (abs.startsWith(r.prefix))
+                return { pid: r.pid, rel: abs.slice(r.prefix.length) };
+        return undefined;
+    };
     for (const pid of wanted) {
         const proj = projects[pid];
         if (!proj)
@@ -166,23 +244,136 @@ export async function canonGraph(o = {}) {
             else
                 edge(nid, projNodeId, 'available_to', 'INFERRED', a._manifestPath);
         }
-        // Optional CODE half: fold an external graphify node-link graph (mode A join).
-        if (o.mergeGraph && fs.existsSync(o.mergeGraph)) {
+        // CODE half (mode A): fold an external graphify node-link graph. An explicit
+        // --merge-graph targets the selected project; otherwise AUTO-DETECT the
+        // standard graphify output at the project root (graphify-out/graph.json —
+        // written by `graphify update <root>`), so keeping the code half fresh is
+        // just re-running graphify; the next canon graph build folds it in.
+        const codeGraphPath = o.mergeGraph && (!o.project || o.project === pid)
+            ? o.mergeGraph
+            : path.join(proj.root, 'graphify-out', 'graph.json');
+        let codeHalf;
+        if (fs.existsSync(codeGraphPath)) {
             try {
-                const g = JSON.parse(fs.readFileSync(o.mergeGraph, 'utf8'));
-                for (const n of g.nodes ?? [])
+                const g = JSON.parse(fs.readFileSync(codeGraphPath, 'utf8'));
+                const gn = g.nodes ?? [];
+                const gl = g.links ?? g.edges ?? [];
+                for (const n of gn)
                     nodes.push(n); // graphify ids are un-namespaced; canon ids can't collide (namespaced)
-                for (const l of g.links ?? g.edges ?? []) {
+                for (const l of gl) {
                     if (l.confidence_score === undefined)
                         l.confidence_score = CONFIDENCE_SCORE[l.confidence ?? 'EXTRACTED'] ?? 1.0;
                     links.push(l);
                 }
+                codeHalf = { source: codeGraphPath, nodes: gn.length, links: gl.length };
             }
             catch { /* malformed external graph — skip, lint covers our own outputs */ }
         }
-        const graph = { directed: true, multigraph: false, graph: {}, nodes, links };
-        if (head)
-            graph.built_at_commit = head;
+        // HISTORY↔CODE JOIN: session→file `touched` edges from the content scan.
+        // Edges route to the OWNING project (longest-root-match): every session —
+        // home or foreign — contributes edges for the paths THIS project owns. A
+        // foreign session (homed elsewhere) gets a marked sess: node here
+        // (foreign_home = its own project) so cross-project work is first-class,
+        // not a tally. Target resolution: prefer the code half's FILE-level node
+        // (source_location L1 + label = basename — graphify's file-node shape);
+        // otherwise a lightweight file: node is created so no touch is dropped.
+        // Paths owned by NO mapped project are tallied (unownedPaths), not edged.
+        let touchedStats;
+        if (touchedIdx) {
+            const fileNodeByPath = new Map();
+            for (const n of nodes) {
+                if (/^(sess|art|proj|file):/.test(n.id))
+                    continue; // code-half nodes only
+                if (n.source_file && n.source_location === 'L1' && n.label === path.basename(n.source_file)) {
+                    if (!fileNodeByPath.has(n.source_file))
+                        fileNodeByPath.set(n.source_file, n.id);
+                }
+            }
+            touchedStats = { edges: 0, inferredEdges: 0, toCodeNodes: 0, toFileNodes: 0, foreignSessions: 0, unownedPaths: 0 };
+            const madeFileNodes = new Map();
+            const presentSessionNodes = new Set(nodes.filter((n) => n.id.startsWith('sess:')).map((n) => n.id));
+            // Edges dedupe by (session node, target): dual-lineage copies of one
+            // session share a uuid — overlapping touches keep the MAX weight
+            // (lineages are copies; summing would double-count).
+            const touchedEdges = new Map();
+            for (const s of sessions) {
+                const home = sessionProject(projects, s);
+                if (home === undefined)
+                    continue;
+                const sessNodeId = `sess:${s.uuid}`;
+                const sessSource = path.join('canon', s.rel);
+                // Pass 1 = tier 1/2 structured evidence (EXTRACTED); pass 2 = tier 3
+                // Bash-parsed paths (INFERRED). Structured evidence wins per edge.
+                for (const [files, inferred] of [
+                    [touchedIdx.byRel.get(s.rel), false],
+                    [touchedIdx.inferredByRel.get(s.rel), true],
+                ]) {
+                    if (!files || files.size === 0)
+                        continue;
+                    for (const [abs, count] of files) {
+                        const owner = ownerOf(abs);
+                        if (!owner) {
+                            if (home === pid && !inferred)
+                                touchedStats.unownedPaths++;
+                            continue;
+                        }
+                        if (owner.pid !== pid)
+                            continue; // routed to the owning project's graph
+                        const rel = owner.rel;
+                        let target = fileNodeByPath.get(rel);
+                        if (target) {
+                            if (!inferred)
+                                touchedStats.toCodeNodes++;
+                        }
+                        else {
+                            target = madeFileNodes.get(rel);
+                            if (!target) {
+                                target = `file:${rel}`;
+                                madeFileNodes.set(rel, target);
+                                nodes.push({ id: target, label: path.basename(rel), file_type: 'document', source_file: rel, source_location: '' });
+                            }
+                            if (!inferred)
+                                touchedStats.toFileNodes++;
+                        }
+                        if (!presentSessionNodes.has(sessNodeId)) {
+                            // Foreign session touching this project's files — first-class, marked.
+                            nodes.push({ id: sessNodeId, label: s.title ?? s.uuid.slice(0, 8), file_type: 'document', source_file: path.join('canon', s.rel), source_location: '', harness: s.harness, foreign_home: home });
+                            presentSessionNodes.add(sessNodeId);
+                            touchedStats.foreignSessions++;
+                        }
+                        const ek = sessNodeId + '|' + target;
+                        const prev = touchedEdges.get(ek);
+                        if (prev) {
+                            if (!inferred) {
+                                prev.weight = Math.max(prev.weight, count);
+                                prev.inferred = false;
+                            }
+                        }
+                        else
+                            touchedEdges.set(ek, { source: sessNodeId, target, weight: count, source_file: sessSource, inferred });
+                    }
+                }
+            }
+            for (const e of touchedEdges.values()) {
+                const conf = e.inferred ? 'INFERRED' : 'EXTRACTED';
+                links.push({ source: e.source, target: e.target, relation: 'touched', confidence: conf, confidence_score: CONFIDENCE_SCORE[conf], source_file: e.source_file, source_location: '', weight: e.weight });
+                if (e.inferred)
+                    touchedStats.inferredEdges++;
+                else
+                    touchedStats.edges++;
+            }
+        }
+        const meta = {};
+        if (codeHalf)
+            meta.code_half = codeHalf;
+        if (touchedStats)
+            meta.touched_stats = touchedStats;
+        // built_at_commit is stamped ONLY when content actually changed — otherwise
+        // every store commit would rewrite the (multi-MB) graph for a HEAD-only
+        // diff, bloating history for zero information (the G2 churn class). The
+        // guard compares the body sans stamp; an unchanged graph keeps its file
+        // (and its original stamp) untouched.
+        const body = { directed: true, multigraph: false, graph: meta, nodes, links };
         totalNodes += nodes.length;
         totalLinks += links.length;
         built.push(pid);
@@ -191,12 +382,27 @@ export async function canonGraph(o = {}) {
             fs.mkdirSync(path.dirname(pj), { recursive: true });
             fs.writeFileSync(pj, JSON.stringify(proj, null, 2) + '\n');
             const gp = path.join(STORE, 'projects', pid, 'graph.json');
-            fs.mkdirSync(path.dirname(gp), { recursive: true });
-            fs.writeFileSync(gp, JSON.stringify(graph, null, 2) + '\n');
+            let unchangedGraph = false;
+            if (fs.existsSync(gp)) {
+                try {
+                    const prev = JSON.parse(fs.readFileSync(gp, 'utf8'));
+                    delete prev.built_at_commit;
+                    unchangedGraph = JSON.stringify(prev) === JSON.stringify(body);
+                }
+                catch { /* rewrite */ }
+            }
+            if (unchangedGraph)
+                unchangedGraphs++;
+            else {
+                if (head)
+                    body.built_at_commit = head;
+                fs.mkdirSync(path.dirname(gp), { recursive: true });
+                fs.writeFileSync(gp, JSON.stringify(body, null, 2) + '\n');
+            }
         }
     }
     let pushed = false;
-    const summary = `${built.length} project graph(s), ${totalNodes} nodes, ${totalLinks} links`;
+    const summary = `${built.length} project graph(s), ${totalNodes} nodes, ${totalLinks} links` + (unchangedGraphs ? `, ${unchangedGraphs} unchanged (stamp kept)` : '');
     if (!o.dryRun) {
         const git = (a) => execFileSync('git', a, { cwd: STORE, encoding: 'utf8', env });
         git(['add', '-A']);

package/dist/canonGraph.js.map

@@ -1 +1 @@
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package/dist/canonInit.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"canonInit.d.ts","sourceRoot":"","sources":["../src/canonInit.ts"],"names":[],"mappings":"AAcA,MAAM,WAAW,gBAAgB;IAC/B,6DAA6D;IAC7D,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,+DAA+D;IAC/D,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,eAAe,EAAE,OAAO,CAAC;IACzB,cAAc,EAAE,OAAO,CAAC;IACxB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;CACnB;AAED,wBAAsB,SAAS,CAAC,OAAO,GAAE,gBAAqB,GAAG,OAAO,CAAC,eAAe,CAAC,CA8CxF"}
+{"version":3,"file":"canonInit.d.ts","sourceRoot":"","sources":["../src/canonInit.ts"],"names":[],"mappings":"AAcA,MAAM,WAAW,gBAAgB;IAC/B,6DAA6D;IAC7D,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,+DAA+D;IAC/D,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,eAAe,EAAE,OAAO,CAAC;IACzB,cAAc,EAAE,OAAO,CAAC;IACxB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;CACnB;AAED,wBAAsB,SAAS,CAAC,OAAO,GAAE,gBAAqB,GAAG,OAAO,CAAC,eAAe,CAAC,CAmDxF"}

package/dist/canonInit.js

@@ -23,8 +23,13 @@ export async function canonInit(options = {}) {
         execFileSync('git', ['init', '-q', '-b', 'main', root], { encoding: 'utf8', env });
         repoInitialized = true;
     }
+    const ROOTS_TEMPLATE = JSON.stringify({
+        _doc: 'Optional project-map overrides for canon graph/list. roots: {projectId: absolutePath}; claudeDirs: {encodedSessionDirName: projectId}; cortexLabels: {cortexSyncLabel: projectId}. Derivation from $HOME + the filesystem covers the common cases; add entries here for dash-ambiguous paths, sessions recorded on other machines, or sub-root labels that belong to a parent project.',
+        roots: {}, claudeDirs: {}, cortexLabels: {},
+    }, null, 2) + '\n';
     const files = [
         ['.gitattributes', GITATTRIBUTES],
+        [path.join('projects', 'ROOTS.json'), ROOTS_TEMPLATE],
         ['README.md', STORE_README],
         [path.join('.github', 'workflows', 'canon-verify.yml'), VERIFY_YML],
         [path.join('.github', 'scripts', 'canon-verify.mjs'), CANON_VERIFY_MJS],

package/dist/canonInit.js.map

@@ -1 +1 @@
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+{"version":3,"file":"canonInit.js","sourceRoot":"","sources":["../src/canonInit.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AACH,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAClD,OAAO,KAAK,EAAE,MAAM,SAAS,CAAC;AAC9B,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAClC,OAAO,EAAE,gBAAgB,EAAE,aAAa,EAAE,UAAU,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAiB5G,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,UAA4B,EAAE;IAC5D,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC;IAC9C,MAAM,OAAO,GAAa,EAAE,CAAC;IAC7B,MAAM,OAAO,GAAa,EAAE,CAAC;IAC7B,MAAM,GAAG,GAAG,EAAE,GAAG,OAAO,CAAC,GAAG,EAAE,mBAAmB,EAAE,GAAG,EAAE,CAAC;IACzD,MAAM,GAAG,GAAG,CAAC,IAAc,EAAE,EAAE,CAAC,YAAY,CAAC,KAAK,EAAE,IAAI,EAAE,EAAE,GAAG,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,CAAC;IAEhG,EAAE,CAAC,SAAS,CAAC,IAAI,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IACxC,IAAI,eAAe,GAAG,KAAK,CAAC;IAC5B,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC,EAAE,CAAC;QAC5C,YAAY,CAAC,KAAK,EAAE,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,CAAC;QACnF,eAAe,GAAG,IAAI,CAAC;IACzB,CAAC;IAED,MAAM,cAAc,GAAG,IAAI,CAAC,SAAS,CAAC;QACpC,IAAI,EAAE,wXAAwX;QAC9X,KAAK,EAAE,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE,YAAY,EAAE,EAAE;KAC5C,EAAE,IAAI,EAAE,CAAC,CAAC,GAAG,IAAI,CAAC;IACnB,MAAM,KAAK,GAAuB;QAChC,CAAC,gBAAgB,EAAE,aAAa,CAAC;QACjC,CAAC,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE,YAAY,CAAC,EAAE,cAAc,CAAC;QACrD,CAAC,WAAW,EAAE,YAAY,CAAC;QAC3B,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,WAAW,EAAE,kBAAkB,CAAC,EAAE,UAAU,CAAC;QACnE,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,SAAS,EAAE,kBAAkB,CAAC,EAAE,gBAAgB,CAAC;KACxE,CAAC;IACF,KAAK,MAAM,CAAC,GAAG,EAAE,OAAO,CAAC,IAAI,KAAK,EAAE,CAAC;QACnC,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;QACjC,IAAI,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YAAC,SAAS;QAAC,CAAC;QACxD,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QACrD,EAAE,CAAC,aAAa,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;QAC/B,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACpB,CAAC;IACD,KAAK,MAAM,GAAG,IAAI,UAAU,EAAE,CAAC;QAC7B,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;QACjC,IAAI,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAAC,OAAO,CAAC,IAAI,CAAC,GAAG,GAAG,GAAG,CAAC,CAAC;YAAC,SAAS;QAAC,CAAC;QAC9D,EAAE,CAAC,SAAS,CAAC,GAAG,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QACvC,EAAE,CAAC,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,UAAU,CAAC,EAAE,EAAE,CAAC,CAAC;QACjD,OAAO,CAAC,IAAI,CAAC,GAAG,GAAG,GAAG,CAAC,CAAC;IAC1B,CAAC;IAED,IAAI,cAAc,GAAG,KAAK,CAAC;IAC3B,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;QACnB,MAAM,SAAS,GAAG,GAAG,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,KAAK,QAAQ,CAAC,CAAC;QACjF,IAAI,SAAS;YAAE,OAAO,CAAC,IAAI,CAAC,6BAA6B,CAAC,CAAC;aACtD,CAAC;YACJ,GAAG,CAAC,CAAC,QAAQ,EAAE,KAAK,EAAE,QAAQ,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC;YACjD,cAAc,GAAG,IAAI,CAAC;YACtB,OAAO,CAAC,IAAI,CAAC,oBAAoB,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;QACrD,CAAC;IACH,CAAC;IACD,OAAO,EAAE,IAAI,EAAE,eAAe,EAAE,cAAc,EAAE,OAAO,EAAE,OAAO,EAAE,CAAC;AACrE,CAAC"}

package/dist/canonPull.d.ts

@@ -1,3 +1,4 @@
+import { type HarnessName } from './canonTools.js';
 export interface CanonStoreOptions {
     /** Canon store working clone (default /tmp/canon-store — off-quota; auto-cloned). */
     store?: string;
@@ -15,6 +16,8 @@ export interface CanonSession {
 export interface CanonPullOptions extends CanonStoreOptions {
     /** Session uuid (or unique prefix) to materialize. */
     session: string;
+    /** Target harness for the tool-compatibility report (default nexus-cortex — where pull lands). */
+    target?: HarnessName;
     /** Destination directory (default {home}/omniclaude-v4/.cortex/sessions). */
     to?: string;
     /** Overwrite an existing local session file (default false — pull is a branch, never a clobber). */

package/dist/canonPull.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"canonPull.d.ts","sourceRoot":"","sources":["../src/canonPull.ts"],"names":[],"mappings":"AAmBA,OAAO,EAAqD,KAAK,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAEtG,MAAM,WAAW,iBAAiB;IAChC,qFAAqF;IACrF,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,sFAAsF;IACtF,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,GAAG,EAAE,MAAM,CAAC;IACZ,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,gBAAiB,SAAQ,iBAAiB;IACzD,sDAAsD;IACtD,OAAO,EAAE,MAAM,CAAC;IAChB,kGAAkG;IAClG,MAAM,CAAC,EAAE,WAAW,CAAC;IACrB,6EAA6E;IAC7E,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,oGAAoG;IACpG,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,eAAe;IAC9B,0EAA0E;IAC1E,IAAI,EAAE,CAAC,GAAG,CAAC,CAAC;IACZ,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,YAAY,CAAC;CACxB;AAcD,kFAAkF;AAClF,wBAAgB,qBAAqB,CAAC,KAAK,EAAE,MAAM,GAAG,YAAY,EAAE,CA2CnE;AAED,qFAAqF;AACrF,wBAAsB,SAAS,CAAC,CAAC,GAAE,iBAAiB,GAAG;IAAE,GAAG,CAAC,EAAE,OAAO,CAAA;CAAO,GAAG,OAAO,CAAC,YAAY,EAAE,CAAC,CAWtG;AAED,qEAAqE;AACrE,wBAAsB,SAAS,CAAC,CAAC,EAAE,gBAAgB,GAAG,OAAO,CAAC,eAAe,CAAC,CAqC7E"}

package/dist/canonPull.js

@@ -17,6 +17,7 @@
 import * as fs from 'node:fs';
 import * as path from 'node:path';
 import { execFileSync } from 'node:child_process';
+import { renderCompat, sessionToolNames, toolCompatibility } from './canonTools.js';
 /** Clone the store if absent, else pull — rehydrate freshness on arrival. */
 function ensureFreshStore(store, repoUrl, label = 'canon-pull') {
     const repo = repoUrl ?? process.env.CANON_REPO ?? 'https://github.com/Spitfire-Products/nexus-canon-store';
@@ -63,8 +64,17 @@ export function discoverCanonSessions(store) {
     for (const [logical, parts] of groups) {
         parts.sort();
         const rel = path.relative(root, logical);
-        const uuid = path.basename(rel, '.jsonl');
+        let uuid = path.basename(rel, '.jsonl');
+        // Dir-per-session envelopes (grok-build: <uuid>/chat_history.jsonl) name
+        // the session by DIRECTORY; adopt the parent when the basename isn't
+        // uuid-ish and the parent is. (claude-code subagents live under a
+        // 'subagents' dir — non-uuid parent — and keep their basename ids.)
+        const parent = path.basename(path.dirname(rel));
+        if (!/^[0-9a-f]{8}-/i.test(uuid) && /^[0-9a-f]{8}-[0-9a-f-]{10,}$/i.test(parent))
+            uuid = parent;
         const bytes = parts.reduce((n, p) => n + fs.statSync(p).size, 0);
+        if (bytes === 0)
+            continue; // empty canon mains (telemetry-only grok sessions) — nothing to pull
         let title;
         const eventsPath = logical.replace(/\.jsonl$/, '.events.jsonl');
         if (fs.existsSync(eventsPath)) {
@@ -128,6 +138,15 @@ export async function canonPull(o) {
     console.log(`[canon-pull] materialized ${s.uuid} (${s.harness}${s.title ? ` — "${s.title}"` : ''})`);
     console.log(`[canon-pull]   ${lines} canonical message(s), ${(s.bytes / 1024).toFixed(0)}KB → ${dest}`);
     console.log(`[canon-pull]   resume with: cortex --resume ${s.uuid} "..."`);
+    // Phase E rung 1: the pull-time tool-ontology compatibility report — the
+    // receiving side learns up front which referenced tools are native, which
+    // map by name, and which need relay/re-expression (P4 ladder).
+    try {
+        const names = await sessionToolNames(dest);
+        if (names.length)
+            console.log(renderCompat(toolCompatibility(names, o.target ?? 'nexus-cortex')));
+    }
+    catch { /* report is best-effort — never block a pull */ }
     return { code: 0, dest, session: s };
 }
 //# sourceMappingURL=canonPull.js.map

package/dist/canonPull.js.map

@@ -1 +1 @@
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package/dist/canonSync.d.ts

@@ -16,5 +16,21 @@ export interface CanonSyncResult {
     scrubbedHits: number;
     pushed: boolean;
 }
+/**
+ * Harness capture sources — DECLARATIVE. Defaults below cover this
+ * environment; `<store>/HARNESSES.json` overrides/extends them:
+ *   { "harnesses": { "<label>": { "exts": [".jsonl"],
+ *       "roots": ["~/.claude/projects"]
+ *              | [{"label":"workspace","path":"~/.cortex/sessions"}] } } }
+ * `~` expands to $HOME. Labeled roots nest under /native/<harness>/<label>/.
+ */
+export interface HarnessSource {
+    exts: string[];
+    roots: (string | {
+        label: string;
+        path: string;
+    })[];
+}
+export declare function loadHarnessSources(store: string, H: string): Record<string, HarnessSource>;
 export declare function canonSync(o?: CanonSyncOptions): Promise<CanonSyncResult>;
 //# sourceMappingURL=canonSync.d.ts.map