@djolex999/vir-cli 0.24.0 → 0.24.3

package/README.md

@@ -5,7 +5,8 @@
 <h1 align="center">vir</h1>
 
 <p align="center">
-  An LLM Wiki for Claude Code, in your Obsidian vault.
+  Karpathy's LLM Wiki, built automatically from your Claude Code sessions.<br>
+  Plain markdown you own: best in Obsidian, fine without it.
 </p>
 
 <p align="center">
@@ -22,7 +23,7 @@ developer-tools, mcp, local-first, cross-platform, llm-wiki
   <a href="https://www.npmjs.com/package/@djolex999/vir-cli"><img src="https://img.shields.io/npm/v/@djolex999/vir-cli?color=7c6af7&label=npm" alt="npm version"></a>
   <a href="https://www.npmjs.com/package/@djolex999/vir-cli"><img src="https://img.shields.io/npm/dw/@djolex999/vir-cli?color=4fd1a0" alt="npm downloads"></a>
   <a href="LICENSE"><img src="https://img.shields.io/badge/license-MIT-22d3ee" alt="license"></a>
-  <a href="#project-status"><img src="https://img.shields.io/badge/tests-612%20passing-22c55e" alt="tests"></a>
+  <a href="#project-status"><img src="https://img.shields.io/badge/tests-1075%20passing-22c55e" alt="tests"></a>
   <a href="#project-status"><img src="https://img.shields.io/badge/platforms-macOS%20%7C%20Linux-lightgrey" alt="platforms"></a>
   <a href="https://modelcontextprotocol.io"><img src="https://img.shields.io/badge/MCP-server-c084fc" alt="mcp"></a>
   <a href="#"><img src="https://img.shields.io/badge/local--first-yes-f59e0b" alt="local-first"></a>
@@ -56,7 +57,7 @@ vir init
 vir run
 ```
 
-`vir init` is a wizard: provider, models, vault path. `vir run` does one pass
+`vir init` is a wizard: provider, models, notes folder. `vir run` does one pass
 over your sessions and writes notes. When you like the output,
 `vir schedule install` registers a daemon that keeps the vault current.
 
@@ -87,7 +88,7 @@ Claude Code sessions
       ↓
      vir
       ↓
-Obsidian vault
+markdown notes (Obsidian vault optional)
       ↓
   CLAUDE.md
       ↓
@@ -112,12 +113,15 @@ Several open source implementations of this pattern now exist
 [nashsu/llm_wiki](https://github.com/nashsu/llm_wiki) among them). Each takes
 a different shape.
 
-Vir is the Obsidian-native one. It treats Obsidian as the primary frontend,
-not just a storage location: a sidebar plugin
+Vir is the one built from your own coding sessions, and it is Obsidian-native
+when you want it. In Obsidian it is a frontend, not just a storage location: a
+sidebar plugin
 ([vir-obsidian](https://github.com/djolex999/vir-obsidian)),
 dataview-compatible frontmatter, wikilinked notes that show up in the graph.
 It reads AI coding session transcripts retroactively, so months of existing
-history become a queryable knowledge base in one run.
+history become a queryable knowledge base in one run. Without Obsidian it is a
+folder of markdown, and `vir query` and the MCP server work with no editor at
+all.
 
 [Karpathy's post →](https://x.com/karpathy/status/2039805659525644595)
 
@@ -141,13 +145,13 @@ worse results, not better."_ Fair. Vir addresses it in layers:
 - **Opt-in `CLAUDE.md` sync.** Nothing vir generates touches your prompt
   context automatically. `vir sync-claude` shows a diff and waits for your
   confirmation. You decide what reaches Claude.
-- **Plain markdown output.** Every note is a file in your Obsidian vault. Read
+- **Plain markdown output.** Every note is a file in your notes folder. Read
   it, edit it, delete it. Nothing is hidden in a database you can't inspect.
 - **Lint and dedupe.** `vir lint` flags contradictions and stale notes;
   `vir dedupe` merges near-duplicate notes that have drifted apart.
 - **Active learning** via `vir review`. Walk through new distillations and
-  approve, edit, or reject each one. Verified notes rank first in retrieval
-  (in `vir query` and the MCP server). Rejected notes move to `.rejected/`,
+  approve, edit, or reject each one. Verified notes get a ranking boost in
+  retrieval (in `vir query` and the MCP server). Rejected notes move to `.rejected/`,
   recoverable, not deleted.
 - **MMR-diverse retrieval.** Queries return notes covering different aspects
   of the topic, not 5 similar duplicates.
@@ -206,8 +210,8 @@ Different tools for different needs:
   capture and vector storage, use claude-mem.
 - **If you're building AI applications that need to remember users**
   long-term, use mem0 (different layer entirely).
-- **If you want an Obsidian-native LLM Wiki** that reads your existing Claude
-  Code sessions, use vir.
+- **If you want an LLM Wiki that reads your existing Claude Code sessions**,
+  Obsidian-native or just a folder of markdown, use vir.
 
 ## Numbers from a real run
 
@@ -224,7 +228,8 @@ Output from my first run across 226 Claude Code sessions:
 
 Other LLM Wiki implementations would produce similar results with the same
 input. The distinguishing question for vir is workflow fit: does
-Obsidian-native plus retroactive match how you actually work?
+retroactive distillation of your own sessions, Obsidian-native when you want
+it, match how you actually work?
 
 Example query against the distilled vault:
 
@@ -255,13 +260,28 @@ sources 4 · via embedding · searched 126
 - macOS or Linux (systemd or cron)
 - Node.js 20+
 - Claude Code (sessions at `~/.claude/projects/`)
-- Obsidian vault
+- A folder for notes. An Obsidian vault works great but is optional; see
+  [Without Obsidian](#without-obsidian).
 - A distill provider — any one of:
   - Anthropic API key (predictable per-session cost, no effect on your Claude Code limits)
   - Your Claude Code subscription (`provider: "claude-cli"` — free and keyless; distills consume your Claude Code usage limits)
   - Kie.ai API key (~72% cheaper, third-party proxy — used for testing and calibration runs, not recommended for your real vault)
 - Optional: Ollama + `nomic-embed-text` for semantic search
 
+
+## Without Obsidian
+
+vir writes plain markdown with YAML frontmatter. Obsidian is the nicest way to
+browse it, but nothing depends on it:
+
+- **Any editor works.** Notes are ordinary `.md` files under `<notes folder>/vir/`.
+  `[[wikilinks]]` read fine as text, and VS Code with Foam or Markdown Memo
+  resolves them as links.
+- **No editor needed for retrieval.** `vir query "<question>"` and the MCP server
+  (`vir mcp install`) search the folder directly.
+- **Point `vir init` at any folder.** If no Obsidian vault exists, it suggests
+  `~/notes` and creates it.
+
 ## Cost
 
 Vir runs two API calls per session: a Haiku classify (cheap) and a distill
@@ -408,8 +428,8 @@ Restart Claude Code. The vault is now queryable mid-session via six tools:
 `vir_query`, `vir_status`, `vir_recent_notes`, `vir_recent_articles`,
 `vir_project_summary`, `vir_compose`. `vir_query` takes a `type` filter
 (`session` | `article` | `topic` | `pdf` | `all`). Human-verified notes
-(approved via `vir review`) rank first; pass `verified_only: true` to see
-only those. The server never writes the vault. `vir_query` is the one tool
+(approved via `vir review`) get a +0.2 score boost; pass `verified_only: true`
+to see only those. The server never writes the vault. `vir_query` is the one tool
 that spends tokens: it synthesizes an answer with your provider, and
 `synthesize: false` returns just the matching notes.
 
@@ -456,7 +476,7 @@ Located at `~/.vir/config.json`.
 
 | Field               | Default                     | Description                                                |
 | ------------------- | --------------------------- | ---------------------------------------------------------- |
-| `vaultPath`         | (required)                  | Absolute path to Obsidian vault                            |
+| `vaultPath`         | (required)                  | Absolute path to your notes folder (Obsidian vault optional) |
 | `outputDir`         | `vir`                       | Subdir inside vault                                        |
 | `claudeProjectsDir` | `~/.claude/projects`        | Claude Code sessions                                       |
 | `cadenceHours`      | `3`                         | Daemon run frequency (hours)                               |
@@ -524,8 +544,8 @@ improvements. Delete it any time; disable it with `"logQueries": false` in
 
 |                |                                           |
 | -------------- | ----------------------------------------- |
-| Version        | 0.22.0                                    |
-| Tests          | 887 passing                               |
+| Version        | 0.24.2                                    |
+| Tests          | 1073 passing                              |
 | Platforms      | macOS (launchd), Linux (systemd/cron)     |
 | Node           | 20+                                       |
 | First-run cost | $1 to $5 (Kie.ai optional, ~72% cheaper)  |
@@ -536,7 +556,7 @@ improvements. Delete it any time; disable it with `"logQueries": false` in
 Shipped:
 
 - [x] Linux support (systemd timer + cron fallback), experimental
-- [x] Active learning: `vir review`, verified notes ranked first in retrieval
+- [x] Active learning: `vir review`, verified notes boosted in retrieval
 - [x] Web article ingestion (Obsidian Web Clipper folder → same vault)
 - [x] PDF and paper ingestion
 - [x] Obsidian plugin: [vir-obsidian](https://github.com/djolex999/vir-obsidian), sidebar queries against the vault

package/dist/cli/costLabel.js

@@ -1,4 +1,4 @@
-import { computeCost } from "../cost/pricing.js";
+import { computeCost, resolvePricing } from "../cost/pricing.js";
 import * as ui from "../ui/display.js";
 // Dollar-estimate label for the ACTIVE provider. On the subscription path the
 // honest label is quota, never "$0.00" — a zero would read as "free API call"
@@ -6,6 +6,9 @@ import * as ui from "../ui/display.js";
 export function estCostLabel(cfg, model, inputTokens, outputTokens) {
     if (cfg.provider === "claude-cli")
         return "subscription quota (no $)";
+    if (resolvePricing(cfg.provider, model, cfg.pricing, cfg.kieTopUpTier) === null) {
+        return `unknown (no price for ${model})`;
+    }
     return ui.formatUsd(computeCost(cfg.provider, model, inputTokens, outputTokens, cfg.pricing, cfg.kieTopUpTier));
 }
 //# sourceMappingURL=costLabel.js.map

package/dist/cli/costLabel.js.map

@@ -1 +1 @@
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package/dist/cli/init.js

@@ -7,11 +7,12 @@ import { homedir } from "node:os";
 import { join } from "node:path";
 import { CONFIG_PATH, maskSecret, ConfigSchema, configExists, ensureVirDir, expandHome, loadConfig, saveConfig, } from "../config.js";
 import { setupNotifications } from "./notificationsSetup.js";
-import { categorizeTranscriptHead, classifyTranscript, estimateSessionCost, groupByProject, readTranscriptHead, } from "../pipeline/projects.js";
+import { categorizeTranscriptHead, estimateSessionCost, readTranscriptHead, } from "../pipeline/projects.js";
+import { buildSources, groupSessions, resolveSource, scanAll, } from "../sources/registry.js";
 import { promptProjectDecisions } from "./projectSelect.js";
-import { scanSessions } from "../pipeline/scanner.js";
 import { normalizeModelName } from "../pipeline/distiller.js";
 import { buildInitConfig } from "./initConfig.js";
+import { defaultNotesDir } from "./notesDir.js";
 import { installToClaudeCode } from "../mcp/install.js";
 import * as ui from "../ui/display.js";
 export async function cmdInit() {
@@ -23,15 +24,14 @@ export async function cmdInit() {
     let vaultPath = "";
     for (;;) {
         vaultPath = await input({
-            message: "Obsidian vault path",
-            default: existing?.vaultPath ??
-                join(homedir(), "Documents", "Obsidian", "MyVault"),
+            message: "Notes folder (any folder of markdown — an Obsidian vault works too)",
+            default: existing?.vaultPath ?? defaultNotesDir(homedir(), existsSync),
         });
         const expanded = expandHome(vaultPath);
         if (existsSync(expanded))
             break;
         const create = await confirm({
-            message: `Vault path does not exist (${expanded}). Create it?`,
+            message: `Folder does not exist (${expanded}). Create it?`,
             default: true,
         });
         if (create) {
@@ -45,7 +45,7 @@ export async function cmdInit() {
         }
     }
     const outputDir = await input({
-        message: "Output subdir inside vault",
+        message: "Output subfolder inside the notes folder",
         default: existing?.outputDir ?? "vir",
     });
     // ── claude projects dir ─────────────────────────────────────────────────
@@ -69,15 +69,14 @@ export async function cmdInit() {
     // ── web articles (optional second input source) ─────────────────────────
     let articlesDir = existing?.articlesDir;
     const wantsArticles = await confirm({
-        message: "Do you save web articles to a folder (e.g. Obsidian Web Clipper)?",
+        message: "Do you save web articles as markdown to a folder (e.g. a web clipper)?",
         default: existing?.articlesDir !== undefined,
     });
     if (wantsArticles) {
         for (;;) {
             articlesDir = await input({
                 message: "Articles (raw/) directory",
-                default: existing?.articlesDir ??
-                    join(homedir(), "Documents", "Obsidian", "raw"),
+                default: existing?.articlesDir ?? join(expandHome(vaultPath), "raw"),
             });
             const expanded = expandHome(articlesDir);
             if (existsSync(expanded))
@@ -255,12 +254,13 @@ export async function cmdInit() {
     let agentTranscriptsAnswer;
     try {
         const projectsDirX = expandHome(claudeProjectsDir);
-        const allFound = scanSessions(projectsDirX);
+        const sources = buildSources({ claudeProjectsDir: projectsDirX });
+        const allFound = scanAll(sources);
         // Triage counts + the agent-transcript question. Only top-level
         // transcripts count (nested workflow/sidechain have their own filter),
         // and agent transcripts are excluded from the per-project multi-select
         // numbers so the costs shown reflect what would actually distill.
-        const topLevel = allFound.filter((s) => classifyTranscript(s.path, projectsDirX) === "session");
+        const topLevel = allFound.filter((s) => resolveSource(sources, s.path).category(s.path) === "session");
         const counts = { interactive: 0, agent: 0, stub: 0 };
         const agentPaths = new Set();
         for (const s of topLevel) {
@@ -287,7 +287,7 @@ export async function cmdInit() {
         const found = agentTranscriptsAnswer !== "include"
             ? topLevel.filter((s) => !agentPaths.has(s.path))
             : topLevel;
-        const groups = [...groupByProject(found, projectsDirX).values()];
+        const groups = [...groupSessions(found, sources).values()];
         if (groups.length > 0) {
             const classifyId = normalizeModelName(classifyModel, provider);
             const distillId = normalizeModelName(distillModel, provider);

package/dist/cli/init.js.map

@@ -1 +1 @@
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package/dist/cli/notesDir.js

@@ -0,0 +1,9 @@
+import { join } from "node:path";
+// vir writes plain markdown; an Obsidian vault is one valid home for it, not a
+// requirement. Prefer the conventional vault when it exists, else ~/notes
+// (notes then land in ~/notes/vir/ via the default outputDir).
+export function defaultNotesDir(home, exists) {
+    const vault = join(home, "Documents", "Obsidian", "MyVault");
+    return exists(vault) ? vault : join(home, "notes");
+}
+//# sourceMappingURL=notesDir.js.map

package/dist/cli/notesDir.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"notesDir.js","sourceRoot":"","sources":["../../src/cli/notesDir.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAEjC,+EAA+E;AAC/E,0EAA0E;AAC1E,+DAA+D;AAC/D,MAAM,UAAU,eAAe,CAC7B,IAAY,EACZ,MAA8B;IAE9B,MAAM,KAAK,GAAG,IAAI,CAAC,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,SAAS,CAAC,CAAC;IAC7D,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;AACrD,CAAC"}

package/dist/cli/projects.js

@@ -1,6 +1,6 @@
-import { classifyTranscript, estimateSessionCost, groupByProject, readTranscriptHead, sniffAgentEntrypoint, } from "../pipeline/projects.js";
+import { estimateSessionCost, } from "../pipeline/projects.js";
 import { normalizeModelName } from "../pipeline/distiller.js";
-import { scanSessions } from "../pipeline/scanner.js";
+import { buildSources, groupSessions, resolveSource, scanAll } from "../sources/registry.js";
 import { StateDb } from "../state/db.js";
 // Aggregate the scan (every project seen on disk) against DB state into the
 // `vir projects` table. Pure — the command wires in scan/DB/config and an
@@ -56,7 +56,8 @@ export function buildProjectsReport(groups, meta, decisions, estCost, nested) {
 // dir, read DB status, apply config decisions. Opens its own StateDb unless
 // one is passed in.
 export function gatherProjectsReport(cfg) {
-    const found = scanSessions(cfg.claudeProjectsDir);
+    const sources = buildSources(cfg);
+    const found = scanAll(sources);
     // Partition out nested agent-internal transcripts (unless the knob says
     // include) so they annotate the table instead of counting as sessions.
     let inScope = found;
@@ -66,7 +67,7 @@ export function gatherProjectsReport(cfg) {
     if (cfg.workflowTranscripts !== "include") {
         inScope = [];
         for (const s of found) {
-            const cat = classifyTranscript(s.path, cfg.claudeProjectsDir);
+            const cat = resolveSource(sources, s.path).category(s.path);
             if (cat === "session")
                 inScope.push(s);
             else {
@@ -79,7 +80,7 @@ export function gatherProjectsReport(cfg) {
     if (cfg.agentTranscripts !== "include") {
         const stillHuman = [];
         for (const s of inScope) {
-            if (sniffAgentEntrypoint(readTranscriptHead(s.path)) !== null) {
+            if (resolveSource(sources, s.path).agentEntrypoint(s.path) !== null) {
                 filteredOut.push(s);
                 catByPath.set(s.path, "agent");
             }
@@ -89,14 +90,14 @@ export function gatherProjectsReport(cfg) {
         }
         inScope = stillHuman;
     }
-    for (const g of groupByProject(filteredOut, cfg.claudeProjectsDir).values()) {
+    for (const g of groupSessions(filteredOut, sources).values()) {
         const counts = { workflow: 0, sidechain: 0, agent: 0 };
         for (const s of g.sessions) {
             counts[catByPath.get(s.path) ?? "sidechain"] += 1;
         }
         nested.set(g.name, counts);
     }
-    const groups = [...groupByProject(inScope, cfg.claudeProjectsDir).values()];
+    const groups = [...groupSessions(inScope, sources).values()];
     // A project whose transcripts are ALL nested would vanish from the table —
     // keep it visible with an empty session group.
     for (const name of nested.keys()) {

package/dist/cli/projects.js.map

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+{"version":3,"file":"projects.js","sourceRoot":"","sources":["../../src/cli/projects.ts"],"names":[],"mappings":"AACA,OAAO,EACL,mBAAmB,GAEpB,MAAM,yBAAyB,CAAC;AACjC,OAAO,EAAE,kBAAkB,EAAE,MAAM,0BAA0B,CAAC;AAC9D,OAAO,EAAE,YAAY,EAAE,aAAa,EAAE,aAAa,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AAC7F,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAC;AAgCzC,4EAA4E;AAC5E,0EAA0E;AAC1E,yCAAyC;AACzC,kDAAkD;AAClD,oEAAoE;AACpE,sEAAsE;AACtE,qEAAqE;AACrE,sCAAsC;AACtC,0EAA0E;AAC1E,MAAM,UAAU,mBAAmB,CACjC,MAAsB,EACtB,IAAsB,EACtB,SAAgD,EAChD,OAAsC,EACtC,MAGC;IAED,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;IACrD,MAAM,IAAI,GAAuB,EAAE,CAAC;IACpC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,WAAW,CAAC;QAClD,MAAM,YAAY,GAAG,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;QACzC,MAAM,GAAG,GAAqB;YAC5B,IAAI,EAAE,CAAC,CAAC,IAAI;YACZ,QAAQ;YACR,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,MAAM;YAC3B,SAAS,EAAE,CAAC;YACZ,OAAO,EAAE,CAAC;YACV,QAAQ,EAAE,CAAC;YACX,cAAc,EAAE,CAAC;YACjB,YAAY,EAAE,EAAE;YAChB,gBAAgB,EAAE,YAAY,EAAE,QAAQ,IAAI,CAAC;YAC7C,iBAAiB,EAAE,YAAY,EAAE,SAAS,IAAI,CAAC;YAC/C,aAAa,EAAE,YAAY,EAAE,KAAK,IAAI,CAAC;SACxC,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YAC3B,MAAM,CAAC,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;YAC7B,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC,UAAU,KAAK,CAAC,EAAE,CAAC;gBAC/C,GAAG,CAAC,SAAS,IAAI,CAAC,CAAC;gBACnB,SAAS;YACX,CAAC;YACD,MAAM,MAAM,GAAG,CAAC,EAAE,UAAU,IAAI,IAAI,CAAC;YACrC,IAAI,MAAM,KAAK,iBAAiB,IAAI,CAAC,CAAC,CAAC,IAAI,QAAQ,KAAK,WAAW,CAAC,EAAE,CAAC;gBACrE,GAAG,CAAC,OAAO,IAAI,CAAC,CAAC;gBACjB,GAAG,CAAC,cAAc,IAAI,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;gBACtC,GAAG,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;YAChC,CAAC;iBAAM,IACL,MAAM,KAAK,kBAAkB;gBAC7B,CAAC,CAAC,CAAC,IAAI,QAAQ,KAAK,SAAS,CAAC,EAC9B,CAAC;gBACD,GAAG,CAAC,QAAQ,IAAI,CAAC,CAAC;YACpB,CAAC;QACH,CAAC;QACD,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACjB,CAAC;IACD,IAAI,CAAC,IAAI,CACP,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,GAAG,CAAC,CAAC,cAAc,IAAI,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAC9E,CAAC;IACF,OAAO,IAAI,CAAC;AACd,CAAC;AAED,4EAA4E;AAC5E,4EAA4E;AAC5E,oBAAoB;AACpB,MAAM,UAAU,oBAAoB,CAAC,GAAW;IAC9C,MAAM,OAAO,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC;IAClC,MAAM,KAAK,GAAG,OAAO,CAAC,OAAO,CAAC,CAAC;IAC/B,wEAAwE;IACxE,uEAAuE;IACvE,IAAI,OAAO,GAAG,KAAK,CAAC;IACpB,MAAM,MAAM,GAAG,IAAI,GAAG,EAGnB,CAAC;IACJ,MAAM,WAAW,GAAiB,EAAE,CAAC;IACrC,MAAM,SAAS,GAAG,IAAI,GAAG,EAA8C,CAAC;IACxE,IAAI,GAAG,CAAC,mBAAmB,KAAK,SAAS,EAAE,CAAC;QAC1C,OAAO,GAAG,EAAE,CAAC;QACb,KAAK,MAAM,CAAC,IAAI,KAAK,EAAE,CAAC;YACtB,MAAM,GAAG,GAAG,aAAa,CAAC,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;YAC5D,IAAI,GAAG,KAAK,SAAS;gBAAE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;iBAClC,CAAC;gBACJ,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;gBACpB,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;YAC7B,CAAC;QACH,CAAC;IACH,CAAC;IACD,yEAAyE;IACzE,IAAI,GAAG,CAAC,gBAAgB,KAAK,SAAS,EAAE,CAAC;QACvC,MAAM,UAAU,GAAiB,EAAE,CAAC;QACpC,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;YACxB,IAAI,aAAa,CAAC,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,IAAI,EAAE,CAAC;gBACpE,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;gBACpB,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;YACjC,CAAC;iBAAM,CAAC;gBACN,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YACrB,CAAC;QACH,CAAC;QACD,OAAO,GAAG,UAAU,CAAC;IACvB,CAAC;IACD,KAAK,MAAM,CAAC,IAAI,aAAa,CAAC,WAAW,EAAE,OAAO,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC;QAC7D,MAAM,MAAM,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC;QACvD,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YAC3B,MAAM,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,WAAW,CAAC,IAAI,CAAC,CAAC;QACpD,CAAC;QACD,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;IAC7B,CAAC;IACD,MAAM,MAAM,GAAG,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;IAC7D,2EAA2E;IAC3E,+CAA+C;IAC/C,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,EAAE,CAAC;QACjC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,IAAI,CAAC,EAAE,CAAC;YACzC,MAAM,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,QAAQ,EAAE,EAAE,EAAE,UAAU,EAAE,CAAC,EAAE,CAAC,CAAC;QACrD,CAAC;IACH,CAAC;IACD,MAAM,EAAE,GAAG,IAAI,OAAO,EAAE,CAAC;IACzB,IAAI,IAAI,CAAC;IACT,IAAI,CAAC;QACH,IAAI,GAAG,EAAE,CAAC,eAAe,EAAE,CAAC;IAC9B,CAAC;YAAS,CAAC;QACT,EAAE,CAAC,KAAK,EAAE,CAAC;IACb,CAAC;IACD,MAAM,UAAU,GAAG,kBAAkB,CAAC,GAAG,CAAC,MAAM,CAAC,QAAQ,EAAE,GAAG,CAAC,QAAQ,CAAC,CAAC;IACzE,MAAM,SAAS,GAAG,kBAAkB,CAAC,GAAG,CAAC,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,QAAQ,CAAC,CAAC;IACvE,OAAO,mBAAmB,CACxB,MAAM,EACN,IAAI,EACJ,GAAG,CAAC,QAAQ,EACZ,CAAC,IAAI,EAAE,EAAE,CACP,mBAAmB,CACjB,GAAG,CAAC,QAAQ,EACZ,UAAU,EACV,SAAS,EACT,IAAI,EACJ,GAAG,CAAC,OAAO,EACX,GAAG,CAAC,YAAY,CACjB,EACH,MAAM,CACP,CAAC;AACJ,CAAC"}

package/dist/cli/reconcile.js

@@ -7,8 +7,8 @@ import { computeCost } from "../cost/pricing.js";
 import { Distiller, normalizeModelName, resolveModelShorthand } from "../pipeline/distiller.js";
 import { ClaudeCliLimitError } from "../pipeline/claudeCli.js";
 import { acquireLock, LockHeldError, releaseLock } from "../pipeline/lock.js";
-import { parseSession } from "../pipeline/parser.js";
-import { projectNameFor } from "../pipeline/projects.js";
+import { decideProject } from "../pipeline/projects.js";
+import { buildSources, resolveSource } from "../sources/registry.js";
 import { scrub } from "../pipeline/scrubber.js";
 import { filterToolCalls } from "../pipeline/toolCallFilter.js";
 import { VaultWriter } from "../pipeline/writer.js";
@@ -38,6 +38,32 @@ export function selectReconcileTargets(rows, force = false) {
             (r.error !== null && r.error !== "")) &&
         (force || (r.attempts ?? 0) < MAX_DISTILL_ATTEMPTS));
 }
+// The filters `vir run` applies before any paid call, in the same order:
+// transcript category, SDK-agent entrypoint, project decision. A row that
+// errored before these existed (or before a project was excluded) must not be
+// retried past them. Returns the skip reason, or null when the row may retry.
+export function reconcileGate(t, cfg) {
+    const source = resolveSource(buildSources(cfg), t.path);
+    if (cfg.workflowTranscripts !== "include") {
+        const cat = source.category(t.path);
+        if (cat !== "session") {
+            return {
+                reason: cat === "workflow" ? "workflow-transcript" : "sidechain-transcript",
+            };
+        }
+    }
+    if (cfg.agentTranscripts !== "include") {
+        const entrypoint = source.agentEntrypoint(t.path);
+        if (entrypoint !== null)
+            return { reason: "agent-transcript", entrypoint };
+    }
+    const decision = decideProject(source.projectName(t.path), cfg.projects ?? {});
+    if (decision === "exclude")
+        return { reason: "project-excluded" };
+    if (decision === "pending")
+        return { reason: "project-pending" };
+    return null;
+}
 // A target whose transcript is gone can't be retried. If an earlier good
 // distill survives (the orphan shape: error set, content kept), the stale
 // error is the only thing hiding that note from listDistilled — clear it.
@@ -48,6 +74,11 @@ export function handleMissingSource(t, clearError) {
     clearError(t.path);
     return "restored";
 }
+// Retry cost for display: the subscription path spends quota, not dollars,
+// so it never shows a misleading $0.
+export function reconcileCostLabel(provider, usd) {
+    return provider === "claude-cli" ? "quota" : ui.formatUsd(usd);
+}
 // Build the per-target summary (cost estimate + collateral flag) without doing
 // any network work. Used by both the dry-run report and the live confirmation.
 export function summarizeReconcileTargets(cfg, targets, costSessionIds, forceDistillModel) {
@@ -62,10 +93,11 @@ export function summarizeReconcileTargets(cfg, targets, costSessionIds, forceDis
         if (hadCostRecord)
             collateralCount += 1;
         let estimatedCost = 0;
+        const missing = !existsSync(t.path);
         // Subscription path: retries cost quota, not dollars — estimate stays 0.
-        if (cfg.provider !== "claude-cli" && existsSync(t.path)) {
+        if (cfg.provider !== "claude-cli" && !missing) {
             try {
-                const parsed = parseSession(t.path, t.hash);
+                const parsed = resolveSource(buildSources(cfg), t.path).parse(t.path, t.hash);
                 const classifyIn = Math.ceil(scrub(parsed.rawSummary).length / CHARS_PER_TOKEN);
                 const distillIn = Math.ceil(scrub(filterToolCalls(parsed.transcriptText, cfg.filterToolCalls).filtered).length / CHARS_PER_TOKEN);
                 estimatedCost =
@@ -82,6 +114,7 @@ export function summarizeReconcileTargets(cfg, targets, costSessionIds, forceDis
             sessionId,
             hadCostRecord,
             estimatedCost,
+            missing,
         });
     }
     return { rows, totalCost, collateralCount };
@@ -119,7 +152,40 @@ export async function runReconcile(cfg, opts = {}) {
     try {
         ui.header(opts.dryRun ? "reconcile  --dry-run" : "reconcile");
         ui.blank();
-        const targets = selectReconcileTargets(db.listReconcileTargets(), opts.force === true);
+        const candidates = selectReconcileTargets(db.listReconcileTargets(), opts.force === true);
+        // Same filters as `vir run`. A gated row leaves the retry list with its
+        // skip reason (it re-enters if the config changes); one that still holds
+        // an earlier good note keeps it, since excluding never touches notes.
+        const targets = [];
+        const gatedBy = new Map();
+        for (const t of candidates) {
+            const gate = existsSync(t.path) ? reconcileGate(t, cfg) : null;
+            if (gate === null) {
+                targets.push(t);
+                continue;
+            }
+            gatedBy.set(gate.reason, (gatedBy.get(gate.reason) ?? 0) + 1);
+            if (opts.dryRun)
+                continue;
+            if (t.content !== null && t.content !== "") {
+                db.keepNote(t.path, t.hash);
+            }
+            else {
+                db.record({
+                    path: t.path,
+                    hash: t.hash,
+                    skipped: true,
+                    notePaths: [],
+                    skipReason: gate.reason,
+                    ...(gate.entrypoint ? { entrypoint: gate.entrypoint } : {}),
+                });
+            }
+        }
+        if (gatedBy.size > 0) {
+            const total = [...gatedBy.values()].reduce((a, b) => a + b, 0);
+            const parts = [...gatedBy.entries()].map(([r, n]) => `${n} ${r}`).join(", ");
+            ui.row(ui.warn(ui.WARN_GLYPH), ui.text(`${total} excluded by the same filters as vir run (${parts})${opts.dryRun ? "" : " — recorded, not retried"}`));
+        }
         if (targets.length === 0) {
             ui.row(ui.success(ui.CHECK), ui.text("nothing to reconcile — every session has content"));
             return;
@@ -140,13 +206,24 @@ export async function runReconcile(cfg, opts = {}) {
         for (const r of rows) {
             const id = r.sessionId.slice(0, 8);
             const marker = r.hadCostRecord ? ui.warn("$") : ui.dim(" ");
-            ui.line(`  ${ui.dim(ui.BULLET)} ${marker} ${ui.text(id.padEnd(10))}  ${ui.dim(`est ${ui.formatUsd(r.estimatedCost)}`)}`);
+            const est = r.missing
+                ? "transcript gone"
+                : `est ${reconcileCostLabel(cfg.provider, r.estimatedCost)}`;
+            ui.line(`  ${ui.dim(ui.BULLET)} ${marker} ${ui.text(id.padEnd(10))}  ${ui.dim(est)}`);
         }
+        const missingCount = rows.filter((r) => r.missing).length;
         ui.blank();
         ui.divider();
         ui.summary({
-            recoverable: { value: rows.length, color: ui.info },
-            "est. retry cost": { value: ui.formatUsd(totalCost), color: ui.warn },
+            recoverable: { value: rows.length - missingCount, color: ui.info },
+            "transcript gone": {
+                value: missingCount,
+                color: missingCount > 0 ? ui.warn : ui.dim,
+            },
+            "est. retry cost": {
+                value: reconcileCostLabel(cfg.provider, totalCost),
+                color: ui.warn,
+            },
             "false-cost collateral": {
                 value: collateralCount,
                 color: collateralCount > 0 ? ui.warn : ui.dim,
@@ -185,7 +262,8 @@ export async function runReconcile(cfg, opts = {}) {
             // are cached but we know their stored content is empty, so we want a
             // forced retry. Parse, score, distill, then update the row in place.
             try {
-                const parsed = parseSession(t.path, t.hash, projectNameFor(t.path, cfg.claudeProjectsDir));
+                const source = resolveSource(buildSources(cfg), t.path);
+                const parsed = source.parse(t.path, t.hash, source.projectName(t.path));
                 const outcome = await distillOneSession(parsed, t, {
                     cfg,
                     db,
@@ -216,11 +294,20 @@ export async function runReconcile(cfg, opts = {}) {
                     process.exitCode = 1;
                     break;
                 }
-                // A retry that fails again must leave the row as-is (content still
-                // null/empty) so the next reconcile pass can catch it. Do NOT mark
-                // it processed-with-empty.
+                // A retry that fails again stays a reconcile target (content still
+                // null/empty, never marked processed-with-empty).
                 stillFailed += 1;
                 const msg = err.message ?? String(err);
+                // Count the failure like vir run does: recordError keeps the row's
+                // hash and content and bumps attempts, so a target that keeps failing
+                // is parked after MAX_DISTILL_ATTEMPTS instead of retried (and paid
+                // for) on every pass. --force still retries parked rows.
+                try {
+                    db.recordError(t.path, t.hash, msg);
+                }
+                catch {
+                    // a bookkeeping failure must not hide the retry result
+                }
                 ui.row(ui.errorColor(ui.CROSS), ui.text(`retry failed: ${deriveSessionId(t.path).slice(0, 8)} — ${msg}`));
             }
         }