oh-my-second-brain 0.3.0 → 0.6.2

package/dist/kernel/engine/axes/store.js

@@ -0,0 +1,422 @@
+import { createHash } from "node:crypto";
+import { mkdir, readFile, readdir, realpath, stat } from "node:fs/promises";
+import path from "node:path";
+import Database from "better-sqlite3";
+import { parseNote } from "../../conventions/frontmatter.js";
+import { excludedNoteMatcher } from "../../conventions/note-exclude.js";
+function isAxisKind(value) {
+    return value === "folder" || value === "field" || value === "link";
+}
+function canonicalAxisKey(value) {
+    const key = value.trim().toLowerCase();
+    if (key.length === 0)
+        throw new Error("Axis key must be non-empty.");
+    return key;
+}
+function scalarType(value) {
+    if (value instanceof Date)
+        return "date";
+    if (typeof value === "string")
+        return "string";
+    if (typeof value === "number")
+        return "number";
+    return "boolean";
+}
+function canonicalScalar(value) {
+    if (value instanceof Date) {
+        if (Number.isNaN(value.getTime()))
+            throw new Error("Axis date value must be valid.");
+        return value.toISOString();
+    }
+    if (typeof value === "string") {
+        const normalized = value.trim().toLowerCase();
+        if (normalized.length === 0)
+            throw new Error("Axis string value must be non-empty.");
+        return normalized;
+    }
+    if (typeof value === "number") {
+        if (!Number.isFinite(value))
+            throw new Error("Axis number value must be finite.");
+        return value;
+    }
+    return value;
+}
+function flattenValue(value) {
+    if (Array.isArray(value))
+        return value.flatMap(flattenValue);
+    if (value instanceof Date || typeof value === "string" || typeof value === "number" || typeof value === "boolean") {
+        return [value];
+    }
+    if (value === null || value === undefined)
+        return [];
+    return [];
+}
+function normalizedLookup(value, type) {
+    if (type === "date")
+        return (value instanceof Date ? value.toISOString() : String(value)).toLowerCase();
+    return String(value).trim().toLowerCase();
+}
+export function normalizeAxisValue(value) {
+    const canonical = canonicalScalar(value);
+    const type = scalarType(value);
+    return { value: canonical, type, normalizedValue: normalizedLookup(canonical, type) };
+}
+function decodeValue(type, json) {
+    let value;
+    try {
+        value = JSON.parse(json);
+    }
+    catch {
+        throw new Error("Axis observation contains invalid stored JSON.");
+    }
+    if (type === "string" && typeof value === "string")
+        return value;
+    if (type === "number" && typeof value === "number" && Number.isFinite(value))
+        return value;
+    if (type === "boolean" && typeof value === "boolean")
+        return value;
+    if (type === "date" && typeof value === "string") {
+        const date = new Date(value);
+        if (!Number.isNaN(date.getTime()))
+            return date;
+    }
+    throw new Error(`Axis observation value does not match stored type ${type}.`);
+}
+function toObservation(row) {
+    if (!isAxisKind(row.axis_kind))
+        throw new Error(`Axis observation has unknown kind ${row.axis_kind}.`);
+    return {
+        notePath: row.note_path,
+        axisKind: row.axis_kind,
+        axisKey: row.axis_key,
+        value: decodeValue(row.value_type, row.value_json),
+        valueType: row.value_type,
+        normalizedValue: row.normalized_value,
+        count: row.count,
+    };
+}
+const CREATE_SCHEMA = `
+  CREATE TABLE IF NOT EXISTS axis_observation (
+    note_path TEXT NOT NULL,
+    axis_kind TEXT NOT NULL CHECK (axis_kind IN ('folder', 'field', 'link')),
+    axis_key TEXT NOT NULL,
+    value_type TEXT NOT NULL CHECK (value_type IN ('string', 'number', 'boolean', 'date')),
+    value_json TEXT NOT NULL,
+    normalized_value TEXT NOT NULL,
+    count INTEGER NOT NULL DEFAULT 1 CHECK (count > 0),
+    PRIMARY KEY (note_path, axis_kind, axis_key, value_type, normalized_value)
+  );
+  CREATE INDEX IF NOT EXISTS axis_observation_lookup
+    ON axis_observation (axis_kind, axis_key, normalized_value);
+  CREATE TABLE IF NOT EXISTS axis_meta (
+    id INTEGER PRIMARY KEY CHECK (id = 1),
+    source_signature TEXT NOT NULL
+  );
+`;
+/** Dedicated EAV repository; never shares the embedding engine database. */
+export class AxisObservationStore {
+    dbPath;
+    db;
+    closed = false;
+    transactionDepth = 0;
+    constructor(dbPath, options = {}) {
+        this.dbPath = dbPath;
+        if (options.readonly === true || options.readOnly === true) {
+            this.db = new Database(dbPath, { readonly: true, fileMustExist: true });
+        }
+        else {
+            this.db = new Database(dbPath);
+            this.db.pragma("journal_mode = WAL");
+            this.db.exec(CREATE_SCHEMA);
+        }
+    }
+    ensureOpen() {
+        if (this.closed)
+            throw new Error("Axis observation store is closed.");
+    }
+    /**
+     * Run a group of writes as one rollback-safe publication. Nested writes from
+     * record/replaceNote participate in the outer transaction rather than
+     * attempting to open a second SQLite transaction.
+     */
+    runInTransaction(fn) {
+        this.ensureOpen();
+        if (this.transactionDepth > 0)
+            return fn();
+        this.transactionDepth += 1;
+        try {
+            return this.db.transaction(fn)();
+        }
+        finally {
+            this.transactionDepth -= 1;
+        }
+    }
+    insertValues(notePath, axisKind, axisKey, value, statement) {
+        for (const original of flattenValue(value)) {
+            // An empty or whitespace-only string carries no axis information, so
+            // it is dropped exactly like the null/undefined that flattenValue
+            // already discards. `field: ""` is a normal "declared but unset"
+            // frontmatter state, not vault corruption; it must not abort the
+            // whole vault scan.
+            if (typeof original === "string" && original.trim().length === 0)
+                continue;
+            let normalized;
+            try {
+                normalized = normalizeAxisValue(original);
+            }
+            catch (error) {
+                // canonicalScalar's own errors carry no note path, which makes them
+                // undiagnosable from the message alone during a whole-vault scan.
+                const message = error instanceof Error ? error.message : String(error);
+                throw new Error(`${notePath}: ${message}`, { cause: error });
+            }
+            statement.run(notePath, axisKind, axisKey, normalized.type, JSON.stringify(normalized.value), normalized.normalizedValue);
+        }
+    }
+    /** Source signature of the markdown set used for the last reconciliation. */
+    sourceSignature() {
+        this.ensureOpen();
+        const row = this.db.prepare("SELECT source_signature FROM axis_meta WHERE id = 1").get();
+        return row?.source_signature ?? null;
+    }
+    setSourceSignature(signature) {
+        this.ensureOpen();
+        this.db.prepare("INSERT INTO axis_meta (id, source_signature) VALUES (1, ?) ON CONFLICT(id) DO UPDATE SET source_signature = excluded.source_signature").run(signature);
+    }
+    /** Record one scalar or every scalar in a frontmatter list. */
+    record(input) {
+        this.ensureOpen();
+        const axisKind = input.axisKind ?? "field";
+        if (!isAxisKind(axisKind))
+            throw new Error(`Unknown axis kind ${String(axisKind)}.`);
+        const axisKey = canonicalAxisKey(input.axisKey);
+        const values = flattenValue(input.value);
+        const statement = this.db.prepare(`
+      INSERT INTO axis_observation
+        (note_path, axis_kind, axis_key, value_type, value_json, normalized_value, count)
+      VALUES (?, ?, ?, ?, ?, ?, 1)
+      ON CONFLICT(note_path, axis_kind, axis_key, value_type, normalized_value)
+      DO UPDATE SET count = axis_observation.count + 1
+    `);
+        this.runInTransaction(() => {
+            for (const value of values)
+                this.insertValues(input.notePath, axisKind, axisKey, value, statement);
+        });
+    }
+    /** Remove all observations for a note, then atomically replace them. */
+    replaceNote(notePath, fields, options = {}) {
+        this.ensureOpen();
+        this.runInTransaction(() => {
+            this.db.prepare("DELETE FROM axis_observation WHERE note_path = ?").run(notePath);
+            const statement = this.db.prepare(`
+        INSERT INTO axis_observation
+          (note_path, axis_kind, axis_key, value_type, value_json, normalized_value, count)
+        VALUES (?, ?, ?, ?, ?, ?, 1)
+        ON CONFLICT(note_path, axis_kind, axis_key, value_type, normalized_value)
+        DO UPDATE SET count = 1
+      `);
+            if (options.folder !== undefined)
+                this.insertValues(notePath, "folder", "folder", options.folder, statement);
+            for (const [axisKey, value] of Object.entries(fields)) {
+                this.insertValues(notePath, "field", canonicalAxisKey(axisKey), value, statement);
+            }
+            for (const link of options.links ?? [])
+                this.insertValues(notePath, "link", "link", link, statement);
+        });
+    }
+    /** Delete stale observations when a markdown note is removed. */
+    deleteNote(notePath) {
+        this.ensureOpen();
+        this.db.prepare("DELETE FROM axis_observation WHERE note_path = ?").run(notePath);
+    }
+    list(options = {}) {
+        this.ensureOpen();
+        const clauses = [];
+        const params = [];
+        if (options.axisKind !== undefined) {
+            if (!isAxisKind(options.axisKind))
+                throw new Error(`Unknown axis kind ${String(options.axisKind)}.`);
+            clauses.push("axis_kind = ?");
+            params.push(options.axisKind);
+        }
+        if (options.axisKey !== undefined) {
+            clauses.push("axis_key = ?");
+            params.push(canonicalAxisKey(options.axisKey));
+        }
+        if (options.notePath !== undefined) {
+            clauses.push("note_path = ?");
+            params.push(options.notePath);
+        }
+        const where = clauses.length === 0 ? "" : ` WHERE ${clauses.join(" AND ")}`;
+        const rows = this.db.prepare(`SELECT note_path, axis_kind, axis_key, value_type, value_json, normalized_value, count
+       FROM axis_observation${where}
+       ORDER BY note_path, axis_kind, axis_key, normalized_value`).all(...params);
+        return rows.map(toObservation);
+    }
+    /** Aggregate facets before any result limit is applied. */
+    facets(options = {}) {
+        const observations = this.list(options);
+        const grouped = new Map();
+        for (const observation of observations) {
+            const id = `${observation.axisKind}\0${observation.axisKey}\0${observation.valueType}\0${observation.normalizedValue}`;
+            const prior = grouped.get(id);
+            if (prior === undefined) {
+                grouped.set(id, {
+                    axisKind: observation.axisKind,
+                    axisKey: observation.axisKey,
+                    value: observation.value,
+                    valueType: observation.valueType,
+                    normalizedValue: observation.normalizedValue,
+                    count: observation.count,
+                });
+            }
+            else {
+                grouped.set(id, { ...prior, count: prior.count + observation.count });
+            }
+        }
+        return [...grouped.values()].sort((left, right) => left.axisKind.localeCompare(right.axisKind) || left.axisKey.localeCompare(right.axisKey) || left.normalizedValue.localeCompare(right.normalizedValue));
+    }
+    count(options = {}) {
+        return this.list(options).reduce((sum, row) => sum + row.count, 0);
+    }
+    close() {
+        if (this.closed)
+            return;
+        this.db.close();
+        this.closed = true;
+    }
+}
+export const openAxisStore = (dbPath, options = {}) => new AxisObservationStore(dbPath, options);
+export function axisStorePath(vault) {
+    return path.resolve(vault, ".oms", "cache", "axes.sqlite");
+}
+export function openVaultAxisStore(vault, options = {}) {
+    return new AxisObservationStore(axisStorePath(vault), options);
+}
+function firstFolder(notePath) {
+    const slash = notePath.indexOf("/");
+    return slash > 0 ? notePath.slice(0, slash) : undefined;
+}
+function extractLinks(body) {
+    const links = [];
+    const pattern = /\[\[([^\]|#]+)(?:[#|][^\]]*)?\]\]/gu;
+    for (const match of body.matchAll(pattern)) {
+        const target = match[1]?.trim();
+        if (target)
+            links.push(target);
+    }
+    return [...new Set(links)];
+}
+const AXIS_SKIP_DIRS = new Set([
+    ".oms",
+    ".obsidian",
+    ".trash",
+    ".git",
+    ".claude",
+    "_archive",
+    "node_modules",
+]);
+function ensureInsideVault(root, candidate, label) {
+    const relative = path.relative(root, candidate);
+    if (relative === ".." || relative.startsWith(`..${path.sep}`) || path.isAbsolute(relative)) {
+        throw new Error(`${label} escapes the configured vault root.`);
+    }
+}
+/**
+ * Strict scanner for EAV reconciliation. The shared convention walker is
+ * intentionally permissive for linting, but a persisted derived snapshot
+ * must fail when a directory/file disappears or a symlink leaves the vault.
+ */
+async function* walkVaultMarkdownStrict(dir, base, isExcluded, rootRealPath, visitedDirectories = new Set()) {
+    const root = rootRealPath ?? await realpath(base);
+    const realDir = await realpath(dir);
+    ensureInsideVault(root, realDir, `Vault directory "${dir}"`);
+    if (visitedDirectories.has(realDir))
+        return;
+    visitedDirectories.add(realDir);
+    const entries = await readdir(dir, { withFileTypes: true });
+    for (const entry of entries) {
+        const fullPath = path.join(dir, entry.name);
+        const realEntry = await realpath(fullPath);
+        ensureInsideVault(root, realEntry, `Vault entry "${fullPath}"`);
+        if (AXIS_SKIP_DIRS.has(entry.name) || entry.name.startsWith("."))
+            continue;
+        const entryStat = await stat(fullPath);
+        if (entryStat.isDirectory()) {
+            yield* walkVaultMarkdownStrict(fullPath, base, isExcluded, root, visitedDirectories);
+        }
+        else if (entryStat.isFile() && entry.name.toLowerCase().endsWith(".md")) {
+            const notePath = path.relative(base, fullPath).replace(/\\/g, "/");
+            // Taxonomy-declared non-notes (template sources above all) never enter
+            // the EAV scan: their frontmatter is intentionally not valid YAML.
+            if (!isExcluded(notePath))
+                yield notePath;
+        }
+    }
+}
+/** Scan markdown into the dedicated EAV cache. Malformed YAML is loud. */
+export async function collectVaultAxisObservations(vault, suppliedStore) {
+    const ownsStore = suppliedStore === undefined;
+    let store = suppliedStore;
+    const liveNotes = new Set();
+    const sourceFiles = new Map();
+    const parsedNotes = [];
+    try {
+        const isExcluded = await excludedNoteMatcher(vault);
+        // Read and parse the complete source set before touching the existing
+        // snapshot. This keeps read/parse failures from exposing a partial scan.
+        for await (const notePath of walkVaultMarkdownStrict(vault, vault, isExcluded)) {
+            const raw = await readFile(path.join(vault, notePath), "utf-8");
+            sourceFiles.set(notePath, Buffer.from(raw, "utf8"));
+            const parsed = parseNote(raw);
+            if (parsed.diagnostics.length > 0) {
+                throw new Error(`${notePath}: malformed frontmatter (${parsed.diagnostics.map((item) => item.message).join("; ")})`);
+            }
+            liveNotes.add(notePath);
+            parsedNotes.push({ notePath, parsed });
+        }
+        const digest = createHash("sha256");
+        for (const notePath of [...sourceFiles.keys()].sort()) {
+            digest.update(notePath);
+            digest.update("\0");
+            digest.update(sourceFiles.get(notePath));
+            digest.update("\0");
+        }
+        // Do not create or open the derived database until the complete source
+        // scan has succeeded. A failed first scan must not publish an empty cache.
+        if (store === undefined) {
+            await ensureAxisStoreDirectory(vault);
+            store = openVaultAxisStore(vault);
+        }
+        const activeStore = store;
+        activeStore.runInTransaction(() => {
+            for (const { notePath, parsed } of parsedNotes) {
+                activeStore.replaceNote(notePath, parsed.frontmatter, {
+                    folder: firstFolder(notePath),
+                    links: extractLinks(parsed.body),
+                });
+            }
+            // A scan is a reconciliation, not an append-only import. Remove rows
+            // for notes that were present in an earlier snapshot but no longer
+            // exist.
+            const staleNotes = new Set(activeStore.list().map((observation) => observation.notePath));
+            for (const notePath of staleNotes) {
+                if (!liveNotes.has(notePath))
+                    activeStore.deleteNote(notePath);
+            }
+            activeStore.setSourceSignature(digest.digest("hex"));
+        });
+        return activeStore;
+    }
+    catch (error) {
+        if (ownsStore)
+            store?.close();
+        throw error;
+    }
+}
+// `mkdir` is intentionally kept in the module so callers can create an empty
+// cache path without touching the embedding engine store.
+export async function ensureAxisStoreDirectory(vault) {
+    await mkdir(path.dirname(axisStorePath(vault)), { recursive: true });
+}
+//# sourceMappingURL=store.js.map

package/dist/kernel/engine/axes/store.js.map

@@ -0,0 +1 @@
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package/dist/kernel/engine/conventions/vault-lint.d.ts

@@ -17,6 +17,7 @@
  *
  * Invalid folder scopes throw clear caller-facing errors; individual notes that cannot be parsed are skipped.
  */
+import { DEFAULT_EXCLUDE_GLOBS, matchesAnyGlob } from "../../conventions/note-exclude.js";
 import type { Concept, Ontology } from "../../ontology/types.js";
 /** One of the five check layers. */
 export type VaultLintRule = "allowlist" | "required" | "type" | "enum" | "routing-law";
@@ -62,9 +63,13 @@ export interface VaultLintOptions {
 /**
  * Default audit exemptions — deliberately not contract violations: build artifacts,
  * self-documenting templates, and skill files that intentionally carry no frontmatter.
+ *
+ * Defined in `../../conventions/note-exclude.js` (below the engine layer) and
+ * re-exported here so existing importers of this module are unaffected; the
+ * scanning walkers that also need this policy (graph builder, EAV axis scan,
+ * graph cache) import it from there directly instead of duplicating it.
  */
-export declare const DEFAULT_EXCLUDE_GLOBS: readonly string[];
-export declare function matchesAnyGlob(notePath: string, globs: readonly string[]): boolean;
+export { DEFAULT_EXCLUDE_GLOBS, matchesAnyGlob };
 /** Merge built-in defaults with vault-declared and caller-supplied exclude globs. */
 export declare function resolveExcludeGlobs(ontology: Ontology, extra?: readonly string[]): string[];
 export declare function validateVaultLintFolder(vaultRoot: string, ontology: Ontology, folder: string | undefined): Promise<void>;

package/dist/kernel/engine/conventions/vault-lint.js

@@ -23,33 +23,19 @@ import { parseNote } from "../../conventions/frontmatter.js";
 import { validateFrontmatter } from "../../conventions/validate.js";
 import { enumViolations, routingLawStrictFolders as writeContractStrictFolders, routingLawViolations, } from "../../conventions/write-contract.js";
 import { walkVaultMarkdown } from "../../conventions/vault-walk.js";
+import { DEFAULT_EXCLUDE_GLOBS, matchesAnyGlob } from "../../conventions/note-exclude.js";
 import { resolveConcept } from "../../ontology/resolver.js";
 // ── Internals ─────────────────────────────────────────────────────────────────
 /**
  * Default audit exemptions — deliberately not contract violations: build artifacts,
  * self-documenting templates, and skill files that intentionally carry no frontmatter.
+ *
+ * Defined in `../../conventions/note-exclude.js` (below the engine layer) and
+ * re-exported here so existing importers of this module are unaffected; the
+ * scanning walkers that also need this policy (graph builder, EAV axis scan,
+ * graph cache) import it from there directly instead of duplicating it.
  */
-export const DEFAULT_EXCLUDE_GLOBS = [
-    "25. Digital Garden/.deploy-staging/**",
-    "**/*.template.md",
-    "**/SKILL.md",
-    ".obsidian/**",
-    ".trash/**",
-    ".oms/**",
-    "_attachments/**",
-];
-/** Convert a `*`/`**` glob into an anchored RegExp. `**` matches across `/`, `*` does not. */
-function globToRegExp(glob) {
-    const GLOBSTAR = "\u0000";
-    const withPlaceholder = glob.replace(/\*\*/g, GLOBSTAR);
-    const escaped = withPlaceholder.replace(/[.+^${}()|[\]\\]/g, "\\$&");
-    const withStar = escaped.replace(/\*/g, "[^/]*");
-    const pattern = withStar.split(GLOBSTAR).join(".*");
-    return new RegExp(`^${pattern}$`);
-}
-export function matchesAnyGlob(notePath, globs) {
-    return globs.some((glob) => globToRegExp(glob).test(notePath));
-}
+export { DEFAULT_EXCLUDE_GLOBS, matchesAnyGlob };
 /** Merge built-in defaults with vault-declared and caller-supplied exclude globs. */
 export function resolveExcludeGlobs(ontology, extra = []) {
     return [...DEFAULT_EXCLUDE_GLOBS, ...(ontology.taxonomy.exclude ?? []), ...extra];

package/dist/kernel/engine/conventions/vault-lint.js.map

@@ -1 +1 @@
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package/dist/kernel/engine/embed/identity.d.ts

@@ -1,11 +1,21 @@
 import { type EmbeddingIdentity } from "./store.js";
+/**
+ * The five model-shape fields are part of the fingerprint.  Provider/model
+ * remain explicit labels as well, so changing either the runtime or model
+ * cannot silently reuse vectors produced by another configuration.
+ */
+export interface EmbeddingShapeIdentity {
+    readonly dimensions: number;
+    readonly contextLength: number;
+    readonly mrlDim: number;
+    readonly normalization: string;
+    readonly prefixScheme: string;
+}
 export declare function fingerprintEmbeddingIdentity(input: {
     provider: string;
     model: string;
-    dimensions: number;
-}): string;
+} & EmbeddingShapeIdentity): string;
 export declare function makeEmbeddingIdentity(input: {
     provider: string;
     model: string;
-    dimensions: number;
-}): EmbeddingIdentity;
+} & EmbeddingShapeIdentity): EmbeddingIdentity;

package/dist/kernel/engine/embed/identity.js

@@ -1,14 +1,46 @@
 import { createHash } from "node:crypto";
 import { ENGINE_EMBED_META_VERSION } from "./store.js";
+function assertShape(input) {
+    if (!Number.isInteger(input.dimensions) || input.dimensions <= 0) {
+        throw new Error("Embedding identity dimensions must be a positive integer.");
+    }
+    if (!Number.isInteger(input.contextLength) || input.contextLength <= 0) {
+        throw new Error("Embedding identity contextLength must be a positive integer.");
+    }
+    if (!Number.isInteger(input.mrlDim) || input.mrlDim < 0) {
+        throw new Error("Embedding identity mrlDim must be a non-negative integer.");
+    }
+    if (typeof input.normalization !== "string" || input.normalization.trim() === "") {
+        throw new Error("Embedding identity normalization is required.");
+    }
+    if (typeof input.prefixScheme !== "string" || input.prefixScheme.trim() === "") {
+        throw new Error("Embedding identity prefixScheme is required.");
+    }
+}
 export function fingerprintEmbeddingIdentity(input) {
-    const raw = [ENGINE_EMBED_META_VERSION, input.provider, input.model, String(input.dimensions)].join("\u0000");
+    assertShape(input);
+    const raw = [
+        ENGINE_EMBED_META_VERSION,
+        input.provider,
+        input.model,
+        String(input.dimensions),
+        String(input.contextLength),
+        String(input.mrlDim),
+        input.normalization,
+        input.prefixScheme,
+    ].join("\u0000");
     return createHash("sha256").update(raw).digest("hex");
 }
 export function makeEmbeddingIdentity(input) {
+    assertShape(input);
     return {
         provider: input.provider,
         model: input.model,
         dimensions: input.dimensions,
+        contextLength: input.contextLength,
+        mrlDim: input.mrlDim,
+        normalization: input.normalization,
+        prefixScheme: input.prefixScheme,
         fingerprint: fingerprintEmbeddingIdentity(input),
     };
 }

package/dist/kernel/engine/embed/identity.js.map

@@ -1 +1 @@
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