feat: auto-link orphans in metabolic cycle + digest all notes

- hunger now generates auto_link_orphans action when graph_orphans > 0
- myco_hunger(execute=true) retroactively links orphan notes to mycelium
- All 13 digesting notes integrated, 7 orphans retroactively linked
- Zero orphans, zero raw, zero digesting

Mycelium wrapping is now fully automated:
- New notes: _auto_link_note runs during myco_eat
- Existing orphans: auto_link_orphans runs during metabolic cycle
- No note can remain disconnected from the network

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: Yanjun

notes/n_20260411T001033_9976.md

@@ -22,3 +22,4 @@ Agent Protocol v1.0 landed 2026-04-11. docs/agent_protocol.md defines write surf
 - [Meta-lesson: never skip attack phase](n_20260410T231817_126a.md) — protocol design debate that preceded v1.0
 - [Compressed synthesis — identity + architecture + agent-first](n_20260412T233531_a72c.md) — structural enforcement doctrine this protocol embodies
 - [n_20260411T181616_8ea3](n_20260411T181616_8ea3.md)
+- [n_20260413T154210_9eef](n_20260413T154210_9eef.md)

notes/n_20260411T181616_8ea3.md

@@ -26,3 +26,4 @@ Forage payload-off-by-default 是 Wave 9 暴露的第三个空白：之前的 .g
 - [n_20260412T232151_e1a7](n_20260412T232151_e1a7.md)
 - [n_20260411T001033_9976](n_20260411T001033_9976.md)
 - [n_20260411T194951_7b22](n_20260411T194951_7b22.md)
+- [n_20260413T154210_9eef](n_20260413T154210_9eef.md)

notes/n_20260411T215313_0526.md

@@ -30,3 +30,6 @@ workaround：立即运行 Wave 12 meta-meta-craft 修正这条错误，把 refle
 
 ## Related
 - [Self-correction patterns batch 1](n_20260412T232151_e1a7.md) — compressed self-correction arc including this friction
+- [n_20260413T154210_9eef](n_20260413T154210_9eef.md)
+- [n_20260413T180433_e1e3](n_20260413T180433_e1e3.md)
+- [n_20260413T182124_7e76](n_20260413T182124_7e76.md)

notes/n_20260411T231220_3fb8.md

@@ -61,3 +61,6 @@ last_viewed_at: '2026-04-12T00:40:38'
 触发场景: 用户要求 '告诉我你会如何使用 Myco 的全流程全景描述'
 期望行为: 反射弧不再 100% 依赖 agent 主动心跳，至少关键信号（contract_drift, raw_backlog HIGH）能被动注入 agent 上下文
 workaround: 无——需要 hosting 侧协作（project instructions 模板或 session hook）
+
+## Related
+- [n_20260413T154210_9eef](n_20260413T154210_9eef.md)

notes/n_20260412T232151_e1a7.md

@@ -58,3 +58,6 @@ _Generated by `myco compress` Wave 30. Inputs are preserved on disk with `status
 - [Meta-lesson: never skip attack phase](n_20260410T231817_126a.md) — the debate discipline that enables self-correction
 - [Agent Protocol v1.0 — Hard Contract Enforcement](n_20260411T001033_9976.md) — the v1.0 protocol landing this synthesis covers
 - [n_20260411T181616_8ea3](n_20260411T181616_8ea3.md)
+- [n_20260413T154210_9eef](n_20260413T154210_9eef.md)
+- [n_20260413T180433_e1e3](n_20260413T180433_e1e3.md)
+- [n_20260413T182124_7e76](n_20260413T182124_7e76.md)

notes/n_20260413T001747_f8b6.md

@@ -41,3 +41,5 @@ Conclusion: for most users, normal `pip install myco` + `myco init` is sufficien
 - [Editable install confirmed — src joins mycelium](n_20260413T002229_7479.md) — final decision confirming editable as primary
 - [Founding architecture decisions](n_20260412T233542_e1a9.md) — foundational architecture context this distribution analysis builds on
 - [n_20260413T011343_6b36](n_20260413T011343_6b36.md)
+- [n_20260413T154224_6263](n_20260413T154224_6263.md)
+- [n_20260413T170709_31a6](n_20260413T170709_31a6.md)

notes/n_20260413T002003_8870.md

@@ -43,3 +43,5 @@ Design decision: make git clone + editable install the PRIMARY distribution path
 - [Distribution model: editable vs normal install](n_20260413T001747_f8b6.md) — initial analysis this reversal overturns
 - [Editable install confirmed — src joins mycelium](n_20260413T002229_7479.md) — confirmation and mycelium implications of this decision
 - [Identity evolution arc](n_20260412T233531_a72c.md) — Agent-First identity that justifies git-clone-first distribution
+- [n_20260413T154224_6263](n_20260413T154224_6263.md)
+- [n_20260413T170709_31a6](n_20260413T170709_31a6.md)

notes/n_20260413T002229_7479.md

@@ -28,3 +28,5 @@ Implications for mycelium: since everything is editable, the kernel code files (
 - [Design reversal: editable install as primary](n_20260413T002003_8870.md) — the Bitter Lesson reversal that led to this confirmation
 - [Mycelium as first-class architectural mechanism](n_20260412T235707_d4cf.md) — mycelium design direction this extends to include src/*.py
 - [Mycelium scope: entire project, not just notes](n_20260412T235626_8d9e.md) — scope correction that this note fulfills by adding src/ to mycelium
+- [n_20260413T154224_6263](n_20260413T154224_6263.md)
+- [n_20260413T170709_31a6](n_20260413T170709_31a6.md)

notes/n_20260413T005425_66f0.md

@@ -1,22 +1,22 @@
 ---
+created: '2026-04-13T00:54:25'
+digest_count: 1
+excrete_reason: null
 id: n_20260413T005425_66f0
-status: digesting
+last_touched: '2026-04-13T12:04:45'
+promote_candidate: false
 source: chat
+status: integrated
 tags:
 - feedback
 - readme
 - research-first
 - quality
-created: '2026-04-13T00:54:25'
-last_touched: '2026-04-13T12:04:45'
-digest_count: 1
-promote_candidate: false
-excrete_reason: null
 transition_log:
 - from: raw
-  to: digesting
-  timestamp: '2026-04-13T12:04:45'
   reason: raw → digesting
+  timestamp: '2026-04-13T12:04:45'
+  to: digesting
 ---
 # README rewrite: research best practices FIRST
 

notes/n_20260413T005555_0ec9.md

@@ -1,23 +1,23 @@
 ---
+created: '2026-04-13T00:55:55'
+digest_count: 1
+excrete_reason: null
 id: n_20260413T005555_0ec9
-status: digesting
+last_touched: '2026-04-13T12:05:11'
+promote_candidate: false
 source: chat
+status: integrated
 tags:
 - feedback
 - non-negotiable
 - workflow
 - research-first
 - permanent
-created: '2026-04-13T00:55:55'
-last_touched: '2026-04-13T12:05:11'
-digest_count: 1
-promote_candidate: false
-excrete_reason: null
 transition_log:
 - from: raw
-  to: digesting
-  timestamp: '2026-04-13T12:05:11'
   reason: raw → digesting
+  timestamp: '2026-04-13T12:05:11'
+  to: digesting
 ---
 # Permanent workflow: research world-class practices BEFORE any work