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Your tools are ready and you know what is in your vault. Let’s explore, find issues, and clean things up — all by describing what you want in natural language.
You can either speak your prompts using Wispr Flow, or type/paste them into Gemini CLI. Both work exactly the same way. Wispr Flow is optional — it just makes the experience hands-free. Every prompt in this tutorial works whether you speak it or type it.

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Search your vault

1

List all files

See every file in your vault at a glance:
Say this or copy this prompt
List all the files in my Obsidian vault
Gemini CLI will show all your notes in a list. Look through and see if anything stands out — files with vague names, notes you forgot about, or duplicates.
2

See your folder structure

Understand how your vault is organised:
Say this or copy this prompt
Show me the folder structure of my Obsidian vault
Are your notes spread across too many folders? Are most notes sitting in the root with no folder at all? This gives you a picture of your vault’s structure.
3

Search for content

Find notes that mention a specific word or phrase:
Say this or copy this prompt
Search my Obsidian vault for any notes that mention the word meeting
Gemini CLI searches the content of every note and returns the ones that mention “meeting”. Try replacing “meeting” with any word you are looking for — a project name, a person’s name, or a topic.
4

Search with context

See the actual matching lines, not just file names:
Say this or copy this prompt
Search my Obsidian vault for notes containing TODO and show me the matching lines, not just file names
This shows you the lines that matched, so you can see exactly what each note says without opening it. Great for finding action items or specific details.
Search works across your entire vault instantly. No more opening notes one by one trying to remember where you wrote something. Just describe what you are looking for and Gemini CLI finds it.

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Audit your tags

1

List all tags

See every tag in your vault and how often each one is used:
Say this or copy this prompt
Show me all the tags in my Obsidian vault, with a count of how many times each tag is used
Look for inconsistencies. Do you have both #meeting and #meetings? What about #mtg? Spotting these variations is the first step to cleaning them up.
2

Get tag details

See exactly which files use a specific tag:
Say this or copy this prompt
Show me which notes use the tag meeting
This shows every note tagged with #meeting. Replace “meeting” with any tag you want to investigate.
Consistent tags make your vault much easier to navigate. If you spot duplicates or variations, note them down. You can ask Gemini CLI to help fix them, or edit the notes directly in Obsidian. Pick one version of each tag and stick with it.

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Find forgotten notes

1

Find orphan notes

Discover notes that nothing links to:
Say this or copy this prompt
Show me all the orphan notes in my Obsidian vault — notes that no other note links to
Orphan notes are notes that exist in your vault but are not connected to anything else. They are often forgotten gems — or notes that need to be linked to related content.
2

Find broken links

Spot links that point to notes that do not exist:
Say this or copy this prompt
Find all the broken links in my vault — links that point to notes that don't exist
This happens when you rename or delete a note but other notes still link to the old name. These are easy to fix once you know about them.
3

Find dead ends

Find notes that do not link to anything else:
Say this or copy this prompt
Show me dead-end notes — notes that don't link to anything else
Dead-end notes might benefit from connections. Could this note link to a related project, person, or topic?
4

Check backlinks

See what links TO a specific note:
Say this or copy this prompt
What notes link to my note called Meeting Notes - March 15?
Backlinks show you the web of connections around a note. If a note has many backlinks, it is an important hub in your vault.
Orphan notes are not necessarily bad — but they represent knowledge that is disconnected from the rest of your vault. Consider asking Gemini CLI to link them to related notes so you can find them again naturally.

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Organise your files

Before moving or renaming files, ask Gemini CLI to read the note first. This helps you avoid accidentally moving the wrong note.
1

Read a note before moving it

Preview a note’s contents without opening Obsidian:
Say this or copy this prompt
Read my note called Untitled and show me what's in it
This shows you exactly what is in the note so you can decide what to do with it — rename it, move it, or leave it where it is.
2

Rename a note

Give a vague note a meaningful name:
Say this or copy this prompt
Rename my note called Untitled to Quick Notes
The note is renamed and all internal links that pointed to “Untitled” are automatically updated. Nothing breaks.
3

Move a note to a folder

Put a note where it belongs:
Say this or copy this prompt
Move my note called Recipe - Banana Bread into a folder called Recipes
Obsidian creates the folder if it does not exist and updates all links that point to this note. Everything stays connected.
4

View a note's outline

See the heading structure without reading the whole note:
Say this or copy this prompt
Show me the heading structure of my note called Meeting Notes - March 15
This is useful for long notes — you can quickly see what sections it contains without scrolling through everything.
5

Check file info

See the details about a specific note:
Say this or copy this prompt
Give me the file info for my note called Quick Notes — when was it created and how big is it?
This shows the file path, size, and when it was created and last modified. Handy for finding notes you have not touched in a while.
When you move or rename a note, Gemini CLI handles link updates automatically. It runs the right Obsidian commands behind the scenes, and Obsidian updates all internal links that point to the file. Nothing breaks — your vault stays connected.

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Go further — try your own requests

You are not limited to the prompts above. Gemini CLI understands a wide range of natural language requests about your vault. Try these:
Say this or copy this prompt
Find all notes in my vault that have no tags
Say this or copy this prompt
Which of my notes is the longest? Show me a word count comparison
Say this or copy this prompt
Search my vault for anything related to career and summarise what I've written about it
Say this or copy this prompt
Are there any duplicate note names in my vault?
Say this or copy this prompt
Show me all notes I created this month
Say this or copy this prompt
List all my notes that contain checkbox tasks, and tell me how many are completed vs incomplete
The key insight: you do not need to memorise commands. Just describe what you want in plain language. Gemini CLI figures out which Obsidian commands to run and handles the details for you.

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Troubleshooting

Make sure the Obsidian CLI plugin is installed and enabled. Run obsidian version in a separate terminal window to check. If it does not return a version number, go back to the setup page and complete Step 3.
This is normal. Gemini CLI asks your permission before running commands on your system. Type y and press Enter to allow it. You can also type always to allow it for the rest of the session.
Wispr Flow may occasionally mishear note names or technical terms. If this happens, try speaking more slowly, or type the prompt instead. You can also correct the transcription before pressing Enter.
Check the note name spelling. Ask Gemini CLI to list all files in your vault to see exact names. Note names do not need file extensions or full paths — just the note title as it appears in Obsidian.
Nice work — your vault is already looking better. Head to Keep going for maintenance habits and more prompts to try.