scientify 1.10.3 → 1.11.0

package/README.md

@@ -336,8 +336,8 @@ You can also check status anytime with:
 | `unpaywall_download` | Download open access PDFs by DOI via Unpaywall API. Non-OA papers are silently skipped (no failure). |
 | `github_search` | Search GitHub repositories. Returns repo name, description, stars, URL. Supports language filtering and sorting. |
 | `paper_browser` | Paginated browsing of large paper files (.tex/.md) to avoid loading thousands of lines into context. Returns specified line range with navigation info. |
-| `scientify_cron_job` | Manage scheduled Scientify jobs from the model (`upsert`/`list`/`remove`). Main fields: `action`, `scope`, `schedule`, `topic`, `message`, `max_papers`, `recency_days`, `candidate_pool`, `score_weights`, `sources`, `channel`, `to`, `no_deliver`, `job_id`. |
-| `scientify_literature_state` | Persistent incremental state for subscriptions: `prepare` dedupe context (+ memory hints), `record` pushed papers, `feedback` lightweight preference memory, and `status` inspection with traceable logs. |
+| `scientify_cron_job` | Manage scheduled Scientify jobs from the model (`upsert`/`list`/`remove`). Main fields: `action`, `scope`, `schedule`, `topic`, `project`, `message`, `max_papers`, `recency_days`, `candidate_pool`, `score_weights`, `sources`, `channel`, `to`, `no_deliver`, `job_id`. |
+| `scientify_literature_state` | Persistent incremental state for subscriptions: `prepare` dedupe context (+ memory hints), `record` pushed papers + project `knowledge_state` artifacts (including `paper_notes` deep-reading fields and full-text cleanup run logs), `feedback` lightweight preference memory, and `status` inspection with traceable logs. |
 
 ### Commands (direct, no LLM)
 
@@ -349,7 +349,7 @@ You can also check status anytime with:
 | `/projects` | List all projects |
 | `/project-switch <id>` | Switch active project |
 | `/project-delete <id>` | Delete a project |
-| `/research-subscribe ...` | Create/update scheduled Scientify jobs (supports `daily`, `weekly`, `every`, `at`, `cron`; options: `--channel`, `--to`, `--topic`, `--message`, `--max-papers`, `--recency-days`, `--candidate-pool`, `--score-weights`, `--sources`, `--no-deliver`) |
+| `/research-subscribe ...` | Create/update scheduled Scientify jobs (supports `daily`, `weekly`, `every`, `at`, `cron`; options: `--channel`, `--to`, `--topic`, `--project`, `--message`, `--max-papers`, `--recency-days`, `--candidate-pool`, `--score-weights`, `--sources`, `--no-deliver`) |
 | `/research-subscriptions` | Show your scheduled Scientify jobs |
 | `/research-unsubscribe [job-id]` | Remove your scheduled Scientify jobs (or a specific job) |
 
@@ -360,6 +360,7 @@ You can also check status anytime with:
 - `/research-subscribe weekly mon 09:30 --channel telegram --to 123456789`
 - `/research-subscribe at 2m --channel webui` (`webui`/`tui` are aliases of `last`)
 - `/research-subscribe daily 08:00 --topic "LLM alignment"`
+- `/research-subscribe daily 08:00 --topic "LLM alignment" --project llm-alignment`
 - `/research-subscribe daily 08:00 --topic "LLM alignment" --max-papers 5 --recency-days 30 --sources arxiv,openalex`
 - `/research-subscribe daily 08:00 --topic "LLM alignment" --candidate-pool 12 --score-weights relevance:45,novelty:20,authority:25,actionability:10`
 - `/research-subscribe at 1m --message "Time to drink coffee."`
@@ -371,9 +372,14 @@ Behavior notes:
 - Reminder-safe fallback: if `topic` looks like a plain reminder (for example "remind me to sleep"), Scientify auto-routes it as a reminder message instead of literature pipeline.
 - One-shot topic (`at ... --topic ...`) uses focused retrieval of representative papers; recurring schedules (`daily/weekly/every/cron`) use incremental tracking mode.
 - Recurring incremental mode uses candidate-pool ranking before Top-K selection; if no unseen paper is found, it runs one representative fallback pass before returning empty.
+- Default `max_papers` is 5 unless overridden by `--max-papers`.
+- Built-in quality gates for research records: core full-text coverage >= 80%, evidence-binding rate >= 90%, citation error rate < 2%. Runs failing gates are downgraded to `degraded_quality`.
 - Lightweight preference memory is stored backend-only (keyword/source affinities) and used to rerank future pushes quietly.
-- Incremental state is persisted under `~/.openclaw/workspace/scientify/` (`literature-state.json`, `literature-push-log.jsonl`) for dedupe + traceability.
-- Storage: subscription jobs are stored in OpenClaw cron storage, not in project workspace files.
+- Incremental dedupe + memory state is persisted under `~/.openclaw/workspace/scientify/` (`literature-state.json`, `literature-push-log.jsonl`).
+- Project-level research traceability is persisted under `~/.openclaw/workspace/projects/{project-id}/knowledge_state/`.
+- Full-text-first scheduled runs store per-paper deep-reading notes (domain/subdomains/cross-domain links/research goal/approach/design/contributions/practical insights/must-understand points/limitations/evidence anchors) under `knowledge_state/paper_notes/`.
+- Full-text files should be downloaded to a temporary directory and cleaned after each run; cleanup result is tracked in `knowledge_state` run logs.
+- Storage: subscription jobs are stored in OpenClaw cron storage; knowledge artifacts are stored in project workspace files.
 - Global inspect: `openclaw cron list --all --json`
 
 ---
@@ -404,9 +410,17 @@ projects/
 │   ├── iterations/                # Review iterations
 │   │   └── judge_v*.md
 │   ├── experiment_res.md          # Final experiment results
-│   └── ideas/                     # Generated ideas
+│   ├── ideas/                     # Generated ideas
 │       ├── idea_*.md
 │       └── selected_idea.md
+│   └── knowledge_state/           # Scheduled research state artifacts
+│       ├── knowledge/
+│       ├── paper_notes/           # Per-paper deep-reading records
+│       ├── daily_changes/
+│       ├── hypotheses/
+│       ├── logs/
+│       ├── state.json
+│       └── events.jsonl
 └── another-project/
 ```
 

package/README.zh.md

@@ -336,8 +336,8 @@ openclaw gateway
 | `unpaywall_download` | 通过 Unpaywall API 按 DOI 下载开放获取 PDF。非 OA 论文跳过不报错。 |
 | `github_search` | 搜索 GitHub 仓库，返回仓库名、描述、star 数、URL。支持语言过滤和排序。 |
 | `paper_browser` | 分页浏览大型论文文件（.tex/.md），避免一次性加载数千行到上下文。返回指定行范围和导航信息。 |
-| `scientify_cron_job` | 由模型管理 Scientify 定时任务（`upsert`/`list`/`remove`）。主要参数：`action`、`scope`、`schedule`、`topic`、`message`、`max_papers`、`recency_days`、`candidate_pool`、`score_weights`、`sources`、`channel`、`to`、`no_deliver`、`job_id`。 |
-| `scientify_literature_state` | 订阅增量状态工具：`prepare` 获取去重上下文（含记忆提示）、`record` 记录已推送论文、`feedback` 写入轻量偏好记忆、`status` 查看状态与可追溯日志。 |
+| `scientify_cron_job` | 由模型管理 Scientify 定时任务（`upsert`/`list`/`remove`）。主要参数：`action`、`scope`、`schedule`、`topic`、`project`、`message`、`max_papers`、`recency_days`、`candidate_pool`、`score_weights`、`sources`、`channel`、`to`、`no_deliver`、`job_id`。 |
+| `scientify_literature_state` | 订阅增量状态工具：`prepare` 获取去重上下文（含记忆提示）、`record` 记录已推送论文 + 项目级 `knowledge_state` 产物（含 `paper_notes` 深读字段与全文临时清理日志）、`feedback` 写入轻量偏好记忆、`status` 查看状态与可追溯日志。 |
 
 ### Commands（直接执行，不经 LLM）
 
@@ -349,7 +349,7 @@ openclaw gateway
 | `/projects` | 列出所有项目 |
 | `/project-switch <id>` | 切换当前项目 |
 | `/project-delete <id>` | 删除项目 |
-| `/research-subscribe ...` | 创建/更新定时 Scientify 任务（支持 `daily`、`weekly`、`every`、`at`、`cron`；可选参数：`--channel`、`--to`、`--topic`、`--message`、`--max-papers`、`--recency-days`、`--candidate-pool`、`--score-weights`、`--sources`、`--no-deliver`） |
+| `/research-subscribe ...` | 创建/更新定时 Scientify 任务（支持 `daily`、`weekly`、`every`、`at`、`cron`；可选参数：`--channel`、`--to`、`--topic`、`--project`、`--message`、`--max-papers`、`--recency-days`、`--candidate-pool`、`--score-weights`、`--sources`、`--no-deliver`） |
 | `/research-subscriptions` | 查看你的 Scientify 定时任务 |
 | `/research-unsubscribe [job-id]` | 取消你的 Scientify 定时任务（或删除指定任务） |
 
@@ -360,6 +360,7 @@ openclaw gateway
 - `/research-subscribe weekly mon 09:30 --channel telegram --to 123456789`
 - `/research-subscribe at 2m --channel webui`（`webui`/`tui` 是 `last` 的别名）
 - `/research-subscribe daily 08:00 --topic "LLM alignment"`
+- `/research-subscribe daily 08:00 --topic "LLM alignment" --project llm-alignment`
 - `/research-subscribe daily 08:00 --topic "LLM alignment" --max-papers 5 --recency-days 30 --sources arxiv,openalex`
 - `/research-subscribe daily 08:00 --topic "LLM alignment" --candidate-pool 12 --score-weights relevance:45,novelty:20,authority:25,actionability:10`
 - `/research-subscribe at 1m --message "Time to drink coffee."`
@@ -371,9 +372,14 @@ openclaw gateway
 - 提醒兜底：如果 `topic` 看起来是普通提醒（例如“提醒我睡觉”），Scientify 会自动按提醒消息处理，不走文献流水线。
 - 一次性研究任务（`at ... --topic ...`）使用“代表论文聚焦检索”；周期任务（`daily/weekly/every/cron`）保持“增量追踪”模式。
 - 周期增量模式会先构建候选池并评分后再选 Top-K；若本轮无“未推送新文献”，会自动再跑一轮代表性回退检索，再决定是否返回空结果。
+- 默认 `max_papers` 为 5（可用 `--max-papers` 覆盖）。
+- 研究记录内置质量闸门：核心论文全文覆盖率 >= 80%、证据绑定率 >= 90%、引用错误率 < 2%。未达标会自动降级为 `degraded_quality`。
 - 轻量偏好记忆（关键词/来源亲和）仅后台保存，不默认展示给用户，会静默影响后续排序。
-- 增量状态会持久化到 `~/.openclaw/workspace/scientify/`（`literature-state.json`、`literature-push-log.jsonl`），用于去重与可追溯。
-- 存储位置：订阅任务保存在 OpenClaw cron 存储中，不写入项目 workspace 文件。
+- 增量去重与偏好状态会持久化到 `~/.openclaw/workspace/scientify/`（`literature-state.json`、`literature-push-log.jsonl`）。
+- 项目级研究可追溯状态会持久化到 `~/.openclaw/workspace/projects/{project-id}/knowledge_state/`。
+- 全文优先的定时研究会在 `knowledge_state/paper_notes/` 中沉淀逐篇深读记录（领域/子领域/交叉领域/研究目标/方法设计/贡献/经验启发/必读要点/局限/证据锚点）。
+- 全文文件建议下载到临时目录并在每轮后清理，清理结果会写入 `knowledge_state` 的 run log。
+- 存储位置：订阅任务保存在 OpenClaw cron 存储中；知识状态产物写入项目 workspace 文件。
 - 全局查看：`openclaw cron list --all --json`
 
 ---
@@ -404,9 +410,17 @@ projects/
 │   ├── iterations/                # 审查迭代
 │   │   └── judge_v*.md
 │   ├── experiment_res.md          # 最终实验结果
-│   └── ideas/                     # 生成的想法
-│       ├── idea_*.md
-│       └── selected_idea.md
+│   ├── ideas/                     # 生成的想法
+│   │   ├── idea_*.md
+│   │   └── selected_idea.md
+│   └── knowledge_state/           # 定时研究状态产物
+│       ├── knowledge/
+│       ├── paper_notes/           # 逐篇深读沉淀
+│       ├── daily_changes/
+│       ├── hypotheses/
+│       ├── logs/
+│       ├── state.json
+│       └── events.jsonl
 └── another-project/
 ```
 

package/dist/src/commands.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"commands.d.ts","sourceRoot":"","sources":["../../src/commands.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,oBAAoB,EAAE,mBAAmB,EAAE,MAAM,UAAU,CAAC;AAwJ1E;;GAEG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CAmDpF;AAED;;GAEG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CAiC3E;AAED;;GAEG;AACH,wBAAgB,WAAW,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CA4B1E;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,oBAAoB,GAAG,mBAAmB,CAqB9E;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CAclF;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,oBAAoB,GAAG,mBAAmB,CA+ClF"}

package/dist/src/commands.js

@@ -76,6 +76,55 @@ function countFiles(dirPath, pattern) {
     }
     return count;
 }
+function getKnowledgeStateSummary(projectId) {
+    const file = path.join(WORKSPACE_ROOT, projectId, "knowledge_state", "state.json");
+    if (!fs.existsSync(file))
+        return null;
+    try {
+        const raw = fs.readFileSync(file, "utf-8");
+        const parsed = JSON.parse(raw);
+        const streams = parsed.streams ?? {};
+        const streamEntries = Object.values(streams);
+        let totalRuns = 0;
+        let totalHypotheses = 0;
+        let totalPaperNotes = 0;
+        let recentFullTextReadCount = 0;
+        let recentNotFullTextReadCount = 0;
+        let lastRunAtMs = 0;
+        let lastStatus;
+        for (const stream of streamEntries) {
+            totalRuns += Number.isFinite(stream.totalRuns) ? Math.max(0, Math.floor(stream.totalRuns)) : 0;
+            totalHypotheses += Number.isFinite(stream.totalHypotheses)
+                ? Math.max(0, Math.floor(stream.totalHypotheses))
+                : 0;
+            totalPaperNotes += Array.isArray(stream.paperNotes) ? stream.paperNotes.length : 0;
+            recentFullTextReadCount += Number.isFinite(stream.recentFullTextReadCount)
+                ? Math.max(0, Math.floor(stream.recentFullTextReadCount))
+                : 0;
+            recentNotFullTextReadCount += Number.isFinite(stream.recentNotFullTextReadCount)
+                ? Math.max(0, Math.floor(stream.recentNotFullTextReadCount))
+                : 0;
+            const runAt = Number.isFinite(stream.lastRunAtMs) ? Math.floor(stream.lastRunAtMs) : 0;
+            if (runAt >= lastRunAtMs) {
+                lastRunAtMs = runAt;
+                lastStatus = stream.lastStatus;
+            }
+        }
+        return {
+            totalRuns,
+            totalHypotheses,
+            totalPaperNotes,
+            recentFullTextReadCount,
+            recentNotFullTextReadCount,
+            ...(lastRunAtMs > 0 ? { lastRunAtMs } : {}),
+            ...(lastStatus ? { lastStatus } : {}),
+            streamCount: streamEntries.length,
+        };
+    }
+    catch {
+        return null;
+    }
+}
 /**
  * /research-status - Show workspace status
  */
@@ -85,6 +134,20 @@ export function handleResearchStatus(_ctx) {
     let output = "📁 **Research Workspace Status**\n\n";
     output += `Root: \`${WORKSPACE_ROOT}\`\n`;
     output += `Active: ${activeProject ? `**${activeProject}**` : "(none)"}\n\n`;
+    if (activeProject) {
+        const knowledgeSummary = getKnowledgeStateSummary(activeProject);
+        if (knowledgeSummary) {
+            output += "**Knowledge State (active project):**\n";
+            output += `- streams: ${knowledgeSummary.streamCount}\n`;
+            output += `- total runs: ${knowledgeSummary.totalRuns}\n`;
+            output += `- total hypotheses: ${knowledgeSummary.totalHypotheses}\n`;
+            output += `- total paper notes: ${knowledgeSummary.totalPaperNotes}\n`;
+            output += `- recent full-text-read papers: ${knowledgeSummary.recentFullTextReadCount}\n`;
+            output += `- recent not-full-text-read papers: ${knowledgeSummary.recentNotFullTextReadCount}\n`;
+            output += `- last status: ${knowledgeSummary.lastStatus ?? "(unknown)"}\n`;
+            output += `- last run: ${knowledgeSummary.lastRunAtMs ? new Date(knowledgeSummary.lastRunAtMs).toISOString() : "(none)"}\n\n`;
+        }
+    }
     if (projects.length === 0) {
         output += "_No projects found. Use /idea-generation to create one._";
     }

package/dist/src/commands.js.map

@@ -1 +1 @@
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package/dist/src/hooks/research-mode.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"research-mode.d.ts","sourceRoot":"","sources":["../../../src/hooks/research-mode.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,KAAK,SAAS,GAAG;IACf,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC;CACtB,CAAC;AAEF,KAAK,WAAW,GAAG;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB,CAAC;AAEF,KAAK,UAAU,GAAG;IAChB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB,CAAC;AAwBF;;GAEG;AACH,wBAAgB,sBAAsB,KAC5B,QAAQ,SAAS,EAAE,UAAU,WAAW,KAAG,UAAU,CAG9D"}
+{"version":3,"file":"research-mode.d.ts","sourceRoot":"","sources":["../../../src/hooks/research-mode.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,KAAK,SAAS,GAAG;IACf,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC;CACtB,CAAC;AAEF,KAAK,WAAW,GAAG;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB,CAAC;AAEF,KAAK,UAAU,GAAG;IAChB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB,CAAC;AA6BF;;GAEG;AACH,wBAAgB,sBAAsB,KAC5B,QAAQ,SAAS,EAAE,UAAU,WAAW,KAAG,UAAU,CAG9D"}

package/dist/src/hooks/research-mode.js

@@ -12,7 +12,12 @@ Workspace: $W/projects/<topic>/. Check /research-status before writing. Active p
   plan_res.md (research-plan) → project/ + ml_res.md (research-implement) → iterations/judge_v*.md (research-review) → experiment_res.md (research-experiment)
 Scheduling: if user asks for recurring or delayed push delivery (e.g. tomorrow at 08:00, daily digest), use research-subscription skill and call scientify_cron_job to create a real schedule.
 If it is a plain reminder (not research), set scientify_cron_job.message and do not default to the literature pipeline.
-For recurring research pushes, use scientify_literature_state to prepare dedupe context and record pushed paper IDs.
+For recurring research pushes, use scientify_literature_state to prepare dedupe context and record both pushed paper IDs and structured knowledge_state (changes, updates, hypotheses, run_log).
+Full-text-first policy: for papers used as core evidence, read full text when possible and mark full_text_read=true; if not fully read, you must explicitly mark full_text_read=false with unread_reason.
+Structured paper record policy: for each core paper, populate domain/subdomains/cross-domain links/research goal/approach/methodology design/key contributions/practical insights/must-understand points/limitations/evidence anchors.
+Use temporary local directory for full-text files (e.g. /tmp/scientify-fulltext/<run-id>) and delete it after record; write cleanup status to run_log.temp_cleanup_status.
+Quality targets for research runs: core full-text coverage >=80%; evidence-binding rate >=90% (key conclusions must bind to section+locator+quote); citation error rate <2%. If full text is missing, do not keep high-confidence conclusions.
+For research records, include project_id when available so state can persist under project knowledge_state/.
 When user gives preference feedback (e.g. "more like this", "skip this direction", "prefer arxiv"), quietly persist it via scientify_literature_state action=feedback when scope/topic are inferable.
 Preference memory is backend-only: use it to rerank future pushes, do not expose memory internals unless user explicitly asks.
 Do not stop at explanation when user explicitly asks to set a schedule.

package/dist/src/hooks/research-mode.js.map

@@ -1 +1 @@
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+{"version":3,"file":"research-mode.js","sourceRoot":"","sources":["../../../src/hooks/research-mode.ts"],"names":[],"mappings":"AAmBA;;GAEG;AACH,MAAM,oBAAoB,GAAG;;;;;;;;;;;;;;;;;;;;;;0NAsB6L,CAAC;AAE3N;;GAEG;AACH,MAAM,UAAU,sBAAsB;IACpC,OAAO,CAAC,MAAiB,EAAE,QAAqB,EAAc,EAAE;QAC9D,OAAO,EAAE,cAAc,EAAE,oBAAoB,EAAE,CAAC;IAClD,CAAC,CAAC;AACJ,CAAC"}

package/dist/src/knowledge-state/project.d.ts

@@ -0,0 +1,13 @@
+export type ProjectContext = {
+    projectId: string;
+    projectPath: string;
+    created: boolean;
+};
+export declare function resolveProjectContext(args: {
+    projectId?: string;
+    scope: string;
+    topic: string;
+    autoCreate?: boolean;
+}): Promise<ProjectContext>;
+export declare function getProjectRootPath(): string;
+//# sourceMappingURL=project.d.ts.map

package/dist/src/knowledge-state/project.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"project.d.ts","sourceRoot":"","sources":["../../../src/knowledge-state/project.ts"],"names":[],"mappings":"AAMA,MAAM,MAAM,cAAc,GAAG;IAC3B,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IACpB,OAAO,EAAE,OAAO,CAAC;CAClB,CAAC;AA4FF,wBAAsB,qBAAqB,CAAC,IAAI,EAAE;IAChD,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,UAAU,CAAC,EAAE,OAAO,CAAC;CACtB,GAAG,OAAO,CAAC,cAAc,CAAC,CAgB1B;AAED,wBAAgB,kBAAkB,IAAI,MAAM,CAE3C"}

package/dist/src/knowledge-state/project.js

@@ -0,0 +1,88 @@
+import { createHash } from "node:crypto";
+import fs from "node:fs";
+import { mkdir, writeFile } from "node:fs/promises";
+import os from "node:os";
+import path from "node:path";
+const PROJECT_ROOT = path.join(os.homedir(), ".openclaw", "workspace", "projects");
+const ACTIVE_PROJECT_FILE = path.join(PROJECT_ROOT, ".active");
+function normalizeText(raw) {
+    return raw.trim().replace(/\s+/g, " ");
+}
+function slugify(raw) {
+    const normalized = normalizeText(raw)
+        .toLowerCase()
+        .replace(/[^a-z0-9_-]+/g, "-")
+        .replace(/-+/g, "-")
+        .replace(/^-|-$/g, "");
+    return normalized || "topic";
+}
+function readActiveProjectId() {
+    try {
+        const raw = fs.readFileSync(ACTIVE_PROJECT_FILE, "utf-8").trim();
+        if (!raw)
+            return undefined;
+        const cleaned = slugify(raw);
+        return cleaned.length > 0 ? cleaned : undefined;
+    }
+    catch {
+        return undefined;
+    }
+}
+function projectExists(projectId) {
+    const projectPath = path.join(PROJECT_ROOT, projectId);
+    return fs.existsSync(projectPath) && fs.statSync(projectPath).isDirectory();
+}
+function deriveAutoProjectId(scope, topic) {
+    const scopeSlug = slugify(scope).slice(0, 18);
+    const topicSlug = slugify(topic).slice(0, 28);
+    const hash = createHash("sha1")
+        .update(`${scope}\n${topic}`)
+        .digest("hex")
+        .slice(0, 6);
+    return `auto-${topicSlug}-${scopeSlug}-${hash}`;
+}
+async function ensureProjectScaffold(projectId, topic) {
+    const projectPath = path.join(PROJECT_ROOT, projectId);
+    if (projectExists(projectId)) {
+        return false;
+    }
+    await mkdir(projectPath, { recursive: true });
+    const createdAt = new Date().toISOString();
+    const projectJsonPath = path.join(projectPath, "project.json");
+    const taskJsonPath = path.join(projectPath, "task.json");
+    if (!fs.existsSync(projectJsonPath)) {
+        await writeFile(projectJsonPath, JSON.stringify({
+            id: projectId,
+            name: topic,
+            created: createdAt,
+            topics: [topic],
+        }, null, 2), "utf-8");
+    }
+    if (!fs.existsSync(taskJsonPath)) {
+        await writeFile(taskJsonPath, JSON.stringify({
+            domain: topic,
+            focus: topic,
+            created: createdAt,
+        }, null, 2), "utf-8");
+    }
+    return true;
+}
+export async function resolveProjectContext(args) {
+    const explicitProjectId = args.projectId ? slugify(args.projectId) : undefined;
+    const activeProjectId = readActiveProjectId();
+    const picked = explicitProjectId || activeProjectId || deriveAutoProjectId(args.scope, args.topic);
+    const autoCreate = args.autoCreate !== false;
+    const created = autoCreate ? await ensureProjectScaffold(picked, args.topic) : false;
+    if (!autoCreate && !projectExists(picked)) {
+        throw new Error(`project not found: ${picked}`);
+    }
+    return {
+        projectId: picked,
+        projectPath: path.join(PROJECT_ROOT, picked),
+        created,
+    };
+}
+export function getProjectRootPath() {
+    return PROJECT_ROOT;
+}
+//# sourceMappingURL=project.js.map

package/dist/src/knowledge-state/project.js.map

@@ -0,0 +1 @@
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package/dist/src/knowledge-state/render.d.ts

@@ -0,0 +1,63 @@
+import type { ExplorationTraceInput, KnowledgeChangeInput, KnowledgeHypothesisInput, KnowledgePaperInput, KnowledgeUpdateInput } from "./types.js";
+export declare function dayKeyFromTimestamp(ts: number): string;
+export declare function slugifyTopic(raw: string): string;
+export declare function renderPaperNoteHeaderMarkdown(args: {
+    paper: KnowledgePaperInput;
+    file: string;
+}): string;
+export declare function renderPaperNoteRunMarkdown(args: {
+    now: string;
+    runId: string;
+    role: "core" | "exploration";
+    paper: KnowledgePaperInput;
+}): string;
+export declare function renderIngestLogMarkdown(args: {
+    now: string;
+    runId: string;
+    scope: string;
+    topic: string;
+    papers: KnowledgePaperInput[];
+}): string;
+export declare function renderExplorationLogMarkdown(args: {
+    now: string;
+    runId: string;
+    trace: ExplorationTraceInput[];
+    papers: KnowledgePaperInput[];
+}): string;
+export declare function renderDailyChangesMarkdown(args: {
+    now: string;
+    runId: string;
+    topic: string;
+    changes: KnowledgeChangeInput[];
+}): string;
+export declare function renderTopicUpdateMarkdown(args: {
+    now: string;
+    runId: string;
+    updates: KnowledgeUpdateInput[];
+}): string;
+export declare function renderHypothesisMarkdown(args: {
+    now: string;
+    hypothesisId: string;
+    runId: string;
+    hypothesis: KnowledgeHypothesisInput;
+}): string;
+export declare function renderKnowledgeIndexMarkdown(args: {
+    now: string;
+    topic: string;
+    topicFiles: string[];
+    paperNotesCount: number;
+    totalHypotheses: number;
+    recentPapers: KnowledgePaperInput[];
+    fullTextReadCount: number;
+    notFullTextReadCount: number;
+    qualityGate: {
+        passed: boolean;
+        fullTextCoveragePct: number;
+        evidenceBindingRatePct: number;
+        citationErrorRatePct: number;
+        reasons: string[];
+    };
+    unreadCorePaperIds: string[];
+    lastStatus?: string;
+}): string;
+//# sourceMappingURL=render.d.ts.map

package/dist/src/knowledge-state/render.d.ts.map

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