obsidian-organizer

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Original

English

🇨🇳

Translation

Chinese

Obsidian Organizer

Obsidian 库整理工具

Keep a large Obsidian vault tidy over time by (1) filing new notes into the best-fit folder and (2) auditing/reorganizing existing structure. Both modes lean on one shared idea: a plain-markdown map of "what goes where" that lives inside the vault so it never drifts out of sync with reality.

This skill drives the

obsidian

CLI (from the separate

obsidian-cli

skill), which talks to the live, running Obsidian desktop app. The app must be open. If a command fails with a connection/vault error, tell the user to open Obsidian rather than guessing.

通过以下两种方式长期保持大型Obsidian库整洁：(1) 将新笔记归档到最适合的文件夹；(2) 审核/重组现有结构。两种模式都基于同一个核心思路：一份存放在库内的纯Markdown格式“内容归属映射”，确保它永远不会与实际库结构脱节。

此功能依赖

obsidian

CLI（来自独立的

obsidian-cli

技能），该CLI与运行中的Obsidian桌面应用通信。应用必须处于打开状态。如果命令因连接/库错误失败，请告知用户打开Obsidian，而非自行猜测。

Why the map lives in the vault (read this first)

为何映射文件要存放在库内（请先阅读此部分）

Deciding a folder for every new note by re-listing ~650 folders is expensive and guesses drift. Copying the folder taxonomy into Claude's private memory creates a worse problem: a stale copy that silently disagrees with the real vault.

The fix is one file,

00_Index/Folder_Map.md

, checked into the vault itself. It is the single source of truth for filing decisions. Read it with one cheap call before you file or reorganize — do not re-run a full

obsidian folders

traversal unless the map is missing or the user asks you to rebuild it.

bash

obsidian read path="00_Index/Folder_Map.md"

It is deliberately plain markdown (headers + bullets, no required frontmatter) so both you and the human can append to it by hand as new categories emerge. When you create a new folder/category, add a line to this file so the next filing decision remembers it.

If the map does not exist (deleted, or a fresh vault), rebuild it from the live vault, not from a copy stashed in this skill — a bundled copy would drift from reality, which is the whole failure this file exists to prevent. List the real structure with

obsidian vault="MyVault" folders

(and

folders folder=...

for depth), draft a plain-markdown map grouped by top-level PARA folder with a short "what goes here" note per folder plus a filing rule-of-thumb, confirm the groupings with the user, then create it:

obsidian vault="MyVault" create path="00_Index/Folder_Map.md" content="..."

为每条新笔记决定文件夹时，重新列出约650个文件夹成本很高，且猜测结果会逐渐偏离实际。将文件夹分类体系复制到Claude的私有内存中会引发更严重的问题：出现与真实库结构不一致的过期副本。

解决方案是使用库内的单个文件

00_Index/Folder_Map.md

，它是归档决策的唯一事实来源。在执行归档或重组操作前，只需通过一次简单调用读取该文件——除非映射文件缺失或用户要求重建，否则不要重新执行完整的
obsidian folders
遍历。

bash

obsidian read path="00_Index/Folder_Map.md"

它特意采用纯Markdown格式（标题+项目符号，无必填前置元数据），以便你和用户都能手动添加新分类。当你创建新文件夹/分类时，需在该文件中添加一行描述，以便后续归档决策能识别它。

如果映射文件不存在（已删除或为全新库），请从运行中的库重建，而非使用此技能中存储的副本——捆绑的副本会与实际情况脱节，而这正是该文件要避免的核心问题。使用

obsidian vault="MyVault" folders

（以及

folders folder=...

指定深度）列出真实结构，草拟一份按顶级PARA文件夹分组的纯Markdown映射，每个文件夹附带简短的“内容归属说明”及归档经验法则，与用户确认分组后再创建该文件：

obsidian vault="MyVault" create path="00_Index/Folder_Map.md" content="..."

。

Vault targeting

库定位

MyVault

above is a placeholder — substitute the user's actual vault name everywhere. If the user has more than one vault, target the intended one explicitly on every command so a stray "most recently focused vault" default cannot misfile a note:

bash

obsidian vault="MyVault" read path="00_Index/Folder_Map.md"

vault=

must be the first parameter. This is the only vault-specific value in the skill — everything else comes from the vault's own

Folder_Map.md

上述

MyVault

是占位符——请在所有位置替换为用户的实际库名称。如果用户有多个库，请在每个命令中明确指定目标库，避免因“最近聚焦的库”默认设置错误归档笔记：

bash

obsidian vault="MyVault" read path="00_Index/Folder_Map.md"

vault=

必须是第一个参数。这是技能中唯一与库相关的固定值——其他所有信息均来自库自身的

Folder_Map.md

。

The one hard safety rule: never touch vault files with raw shell

唯一硬性安全规则：永远不要用原生Shell操作库文件

When you relocate or rename a file, always use the CLI's own

move

rename

commands. These go through Obsidian's API, so Obsidian's built-in "automatically update internal links" behavior rewrites every wikilink and backlink across the vault to follow the moved file. A raw

mv

rm

rmdir

, or

find -delete

on a path inside the vault skips that repair and silently leaves broken links pointing at the old location.

So, for anything under the vault directory:

Move/rename →
```
obsidian move ...
```
or
```
obsidian rename ...
```
Delete →
```
obsidian delete ...
```
(sends to trash unless
```
permanent
```
)
Never use Bash
```
mv
```
/
```
rm
```
/
```
rmdir
```
/
```
find -delete
```
on vault-internal paths.

Reading a file's bytes with a non-mutating tool is fine; mutating vault files is CLI-only.

当你移动或重命名文件时，务必使用CLI自带的
move
/
rename
命令。这些命令通过Obsidian的API执行，因此Obsidian内置的“自动更新内部链接”功能会重写库中所有维基链接和反向链接，使其指向移动后的文件。直接使用原生Shell的

mv

、

rm

、

rmdir

或

find -delete

操作库内路径会跳过此修复步骤，导致链接静默指向旧位置并失效。

因此，对于库目录下的所有操作：

移动/重命名 → 使用
```
obsidian move ...
```
或
```
obsidian rename ...
```
删除 → 使用
```
obsidian delete ...
```
（除非指定
```
permanent
```
，否则会移至回收站）
绝对不要对库内路径使用Bash的
```
mv
```
/
```
rm
```
/
```
rmdir
```
/
```
find -delete
```
命令。

使用非修改工具读取文件内容是允许的；修改库文件必须通过CLI执行。

Mode 1 — File a note

模式1 — 归档笔记

Goal: given a note (an existing path, or a title + content you're about to write), put it in the single best-fit folder.

Read the map once:

obsidian vault="MyVault" read path="00_Index/Folder_Map.md"

Match the note's topic to a destination using the map's filing rules. Favor an existing specific subfolder over a general one (e.g. a Seurat how-to goes to
```
03_Research_Knowledge/Bioinformatics/seurat/
```
, not a generic bucket).
Act on the best fit:
- A clearly matching folder exists → file it there.
  - New note:
```
obsidian vault="MyVault" create path="03_Research_Knowledge/Bioinformatics/seurat/My Note.md" content="..." silent
```
  - Existing note to relocate:
```
obsidian vault="MyVault" move path="00_Inbox/My Note.md" to="03_Research_Knowledge/Bioinformatics/seurat"
```
    (
```
to
```
    may be a folder or a full path).
- A rough-but-imperfect fit exists (e.g. a tool with no dedicated subfolder) → use the map's catch-all convention (e.g.
```
Bioinformatics/misc/
```
  ) and tell the user where it went.
- No category fits well → stop and ask the user before inventing a folder. Propose a name and location; don't silently create new taxonomy.
Remember new categories. When the user approves a new folder, append a line describing it under the right section of
```
00_Index/Folder_Map.md
```
(
```
obsidian append path="00_Index/Folder_Map.md" content="..."
```
) so future filing decisions know about it.
Briefly report the final path.

Notes on the CLI:

create

makes intermediate folders as needed; add

silent

so it doesn't steal focus by opening the note.

move

to

accepts a destination folder or a full path; use

rename name="New Title"

to change a title in place.

目标：给定一条笔记（现有路径，或你即将写入的标题+内容），将其放入唯一最合适的文件夹。

读取映射文件一次：

obsidian vault="MyVault" read path="00_Index/Folder_Map.md"

。

匹配笔记主题与映射文件中的归档规则对应的目标文件夹。优先选择现有的特定子文件夹而非通用文件夹（例如，Seurat操作指南应放入
```
03_Research_Knowledge/Bioinformatics/seurat/
```
，而非通用分类）。
根据最佳匹配执行操作：
- 存在明确匹配的文件夹 → 将笔记归档至该文件夹。
  - 新笔记：
```
obsidian vault="MyVault" create path="03_Research_Knowledge/Bioinformatics/seurat/My Note.md" content="..." silent
```
  - 需迁移的现有笔记：
```
obsidian vault="MyVault" move path="00_Inbox/My Note.md" to="03_Research_Knowledge/Bioinformatics/seurat"
```
    （
```
to
```
    可以是文件夹路径或完整文件路径）。
- 存在大致匹配但不够精准的文件夹（例如，某工具无专用子文件夹） → 使用映射文件中的兜底规则（例如
```
Bioinformatics/misc/
```
  ），并告知用户笔记存放位置。
- 无合适分类 → 停止操作并询问用户，不要自行创建文件夹。建议文件夹名称和位置；不要静默创建新分类体系。
记录新分类。当用户批准新文件夹后，在
```
00_Index/Folder_Map.md
```
的对应章节添加一行描述（
```
obsidian append path="00_Index/Folder_Map.md" content="..."
```
），以便后续归档决策能识别它。
简要报告最终路径。

CLI使用说明：

create

命令会自动创建所需的中间文件夹；添加

silent

参数可避免打开笔记而占用焦点。

move

命令的

to

参数接受目标文件夹或完整路径；使用

rename name="New Title"

可原地修改标题。

Mode 2 — Audit / reorganize

模式2 — 审核/重组

Goal: given a scope (a folder path, "recent inbox notes", or an explicit request like "clean up the cellchat notes"), find problems, propose a plan, get explicit confirmation, then execute. Never move, merge, or delete in bulk silently.

目标：给定范围（文件夹路径、“最近的收件箱笔记”或明确请求如“整理CellChat相关笔记”），找出问题，提出计划，获取明确确认后再执行。永远不要静默批量移动、合并或删除文件。

Step 1 — Gather signals for the scope

步骤1 — 收集范围内的信号

Read the map first for context, then use the structural commands. Scope every list to the folder in question where the command supports it.

```
obsidian vault="MyVault" files folder="<scope>"
```
— inventory + spot near-duplicate titles (e.g. "CellChat analysis" vs "CellChat Analysis v2").
```
obsidian vault="MyVault" orphans
```
— notes with no incoming links (nothing links to them; candidates for filing/merging/archiving).
```
obsidian vault="MyVault" deadends
```
— notes with no outgoing links (often stubs or captures that were never developed).
```
obsidian vault="MyVault" search:context query="<topic>" path="<scope>"
```
— compare content of suspected near-duplicates before proposing a merge.
```
obsidian vault="MyVault" backlinks path="<file>"
```
— before merging or deleting a note, see what links to it so you don't strand references.

There is no dedicated "duplicates" command; detect duplicates by comparing the titles from

files

and confirming with

search:context

read

先读取映射文件获取上下文，再使用结构命令。在命令支持的情况下，将所有列表限定在指定范围内。

```
obsidian vault="MyVault" files folder="<scope>"
```
— 列出文件清单并识别标题近似重复的笔记（例如“CellChat analysis”与“CellChat Analysis v2”）。
```
obsidian vault="MyVault" orphans
```
— 无 incoming链接的笔记（没有任何内容链接到它们；可作为归档/合并/存档的候选对象）。
```
obsidian vault="MyVault" deadends
```
— 无 outgoing链接的笔记（通常是未完善的草稿或临时记录）。
```
obsidian vault="MyVault" search:context query="<topic>" path="<scope>"
```
— 在提出合并建议前，对比疑似近似重复笔记的内容。
```
obsidian vault="MyVault" backlinks path="<file>"
```
— 在合并或删除笔记前，查看哪些内容链接到它，避免失效引用。

没有专门的“重复项”检测命令；需通过

files

命令获取标题并结合

search:context

read

命令确认来检测重复项。

Step 2 — Propose a plan (and wait)

步骤2 — 提出计划（等待确认）

Present a concrete, itemized plan and stop for confirmation. Group by action:

Proposed reorganization for Bioinformatics/cellchat/ (7 notes):

MERGE
- "CellChat analysis.md" + "CellChat analysis (1).md" → keep "CellChat analysis.md",
  fold unique content from the duplicate in, then delete the duplicate.

MOVE
- "Spatial CellChat.md" → Single_Cell/Spatial_Omics/ (topic is spatial, not the tool)

RENAME
- "untitled cellchat.md" → "CellChat LR database notes.md"

No change: 3 notes look fine.

Proceed? I won't move/merge/delete anything until you confirm.

Keep the plan honest about uncertainty — flag guesses so the user can veto them.

呈现具体的分项计划并等待确认。按操作类型分组：

针对Bioinformatics/cellchat/的重组建议（共7条笔记）：

合并
- "CellChat analysis.md" + "CellChat analysis (1).md" → 保留"CellChat analysis.md"，将重复笔记中的独特内容合并进去，然后删除重复笔记。

移动
- "Spatial CellChat.md" → Single_Cell/Spatial_Omics/（主题是空间组学，而非工具本身）

重命名
- "untitled cellchat.md" → "CellChat LR数据库笔记.md"

无变动：3条笔记状态良好。

是否执行？在你确认前，我不会进行任何移动/合并/删除操作。

如实说明计划中的不确定之处——标记猜测内容，以便用户可以否决。

Step 3 — Execute only after "yes"

步骤3 — 仅在用户确认“是”后执行

On confirmation, run the moves/renames/deletes through the CLI in the order that keeps links intact (usually: merge content first, then delete the emptied duplicate; move before rename if both apply). Use

move

rename

delete

append

read

for merges — never raw shell. Report what changed, and append any new folders/categories you created to

00_Index/Folder_Map.md

获得确认后，通过CLI按保持链接有效的顺序执行移动/重命名/删除操作（通常：先合并内容，再删除已清空的重复笔记；若同时需要移动和重命名，先移动后重命名）。使用

move

、

rename

、

delete

、

append

read

命令执行合并操作——永远不要使用原生Shell。报告已更改的内容，并将创建的任何新文件夹/分类添加到

00_Index/Folder_Map.md

中。

Known standing reorg candidates

已知待重组候选对象

If the vault's

Folder_Map.md

calls out known problem areas (legacy folders that overlap a newer one, a subfolder with accumulated near-duplicate titles, etc.), surface them when they're in scope — but still propose-and-confirm before touching anything.

如果库的

Folder_Map.md

指出了已知问题区域（与新分类重叠的旧文件夹、积累了大量近似重复标题的子文件夹等），当这些区域在范围内时需指出——但仍需先提出计划并获得确认，再进行任何操作。

Command quick reference

命令速查

Need	Command
Read the map	`obsidian vault="MyVault" read path="00_Index/Folder_Map.md"`
Create/file a new note	`obsidian vault="MyVault" create path="Folder/Note.md" content="..." silent`
Move/relocate a note	`obsidian vault="MyVault" move path="Old/Note.md" to="New/Folder"`
Rename in place	`obsidian vault="MyVault" rename path="Folder/Note.md" name="New Title"`
Delete (to trash)	`obsidian vault="MyVault" delete path="Folder/Note.md"`
List files in a folder	`obsidian vault="MyVault" files folder="<scope>"`
Orphans / dead-ends	`obsidian vault="MyVault" orphans` · `... deadends`
Search with context	`obsidian vault="MyVault" search:context query="..." path="<scope>"`
Backlinks to a note	`obsidian vault="MyVault" backlinks path="Folder/Note.md"`
Append to the map	`obsidian vault="MyVault" append path="00_Index/Folder_Map.md" content="- ..."`

Run

obsidian help <command>

to confirm exact params — the CLI is the ground truth.

需求	命令
读取映射文件	`obsidian vault="MyVault" read path="00_Index/Folder_Map.md"`
创建/归档新笔记	`obsidian vault="MyVault" create path="Folder/Note.md" content="..." silent`
移动/迁移笔记	`obsidian vault="MyVault" move path="Old/Note.md" to="New/Folder"`
原地重命名	`obsidian vault="MyVault" rename path="Folder/Note.md" name="New Title"`
删除（移至回收站）	`obsidian vault="MyVault" delete path="Folder/Note.md"`
列出文件夹内的文件	`obsidian vault="MyVault" files folder="<scope>"`
孤立笔记/无后续链接笔记	`obsidian vault="MyVault" orphans` · `... deadends`
带上下文的搜索	`obsidian vault="MyVault" search:context query="..." path="<scope>"`
笔记的反向链接	`obsidian vault="MyVault" backlinks path="Folder/Note.md"`
追加内容到映射文件	`obsidian vault="MyVault" append path="00_Index/Folder_Map.md" content="- ..."`

运行

obsidian help <command>

确认准确参数——CLI是最终依据。