Vault Search and Indexing
Configure lexical and semantic vault search, indexing, exclusions, and Miyo.
Copilot can search your vault to find relevant notes and answer questions grounded in your own content. This guide explains the two types of search, how to manage the index, and how to configure what gets indexed.
Two Types of Search
Lexical Search (Keyword-Based)
Lexical search finds notes that contain the exact words you used. It's fast, requires no setup, and works out of the box.
- Used in: Vault QA (Basic) mode
- How it works: Looks for your exact keywords in note titles and content
- Strengths: Fast, precise, no embedding API calls needed
- Limitations: Won't find notes that use different words to express the same idea
RAM Limit: The lexical search index is held in memory. You can configure the memory limit in Settings → Copilot → QA → Lexical Search RAM Limit (default: 100 MB, range: 20–1,000 MB).
Lexical Boosts: Copilot can boost search results from notes in the same folder as the current note, or from notes that link to each other. Enable in Settings → Copilot → QA → Enable Lexical Boosts (on by default).
Semantic Search (Meaning-Based)
Semantic search finds notes that are conceptually related, even if they don't share exact words.
- Used in: Vault QA and paid Quick Chat — but disabled by default. You must explicitly enable it.
- How it works: Converts your notes into numerical vectors (using an embedding model), then finds notes whose vectors are closest to your query
- Strengths: Finds notes by concept and meaning, great for "fuzzy" recall
- Cost: Requires embedding API calls (costs money for paid embedding models)
- Enable: Settings → Copilot → QA → Enable Semantic Search — turn this on to activate semantic search
Index Management
The semantic search index stores the vector embeddings of your notes. Manage it from Settings → Copilot → QA.
Auto-Index Strategy
Controls when Copilot automatically updates the index:
| Strategy | When the index updates |
|---|---|
| NEVER | Manual only — you must trigger indexing yourself |
| ON STARTUP | Updates when Obsidian starts or the plugin reloads |
| ON MODE SWITCH | Updates when you switch to Vault QA or paid Quick Chat (Recommended) |
The default is ON MODE SWITCH.
Warning: For large vaults using paid embedding models, frequent indexing can incur significant costs. Consider using NEVER and indexing manually if cost is a concern.
Refresh Index (Incremental)
Command palette → Index (refresh) vault
Updates only notes that have been added, modified, or deleted since the last index. Faster and cheaper than a full reindex.
Force Reindex
Command palette → Force reindex vault
Rebuilds the entire index from scratch. Use this if:
- You changed your embedding model
- The index seems corrupted or missing results
- You've made many changes and want a clean state
Garbage Collection
Command palette → Garbage collect Copilot index (remove files that no longer exist in vault)
Removes entries from the index for notes that have been deleted from your vault. Keeps the index clean without a full reindex.
Clear Index
Command palette → Clear local Copilot index
Deletes the entire index. You'll need to reindex before semantic search works again.
Debug Commands
For troubleshooting:
- List indexed files — Shows all notes currently in the index
- Inspect index by note paths — Check which chunks of specific notes are indexed
- Count total vault tokens — Estimates total tokens across your vault
- Search semantic index — Run a direct search query against the index
Filtering: What Gets Indexed
Control which notes are included in semantic search.
Cost Estimation Before Indexing
Before indexing a large vault with a paid embedding model, estimate the cost first:
Command palette → Count total tokens in your vault
This shows the total token count across your vault, which you can use to estimate embedding API costs. Embedding costs are generally low, but worth checking for very large vaults.
Exclusions
Settings → Copilot → QA → Exclusions
Comma-separated list of patterns. Notes matching these patterns are excluded. Supports:
- Folder names:
private— excludes the folder named "private" - Folder paths:
Work/Confidential— excludes that specific subfolder - File extensions:
.pdf— excludes all PDF files - Tags:
#private— excludes all notes tagged#private - Note titles:
My Secret Note— excludes that specific note
Example: private, Work/Confidential, #private excludes the private folder, a specific work folder, and all notes tagged #private.
Note: Tag matching works with tags in the note's properties (frontmatter), not inline tags within the note body.
Your Copilot folder is always excluded automatically (it holds the plugin's own files — conversations, prompts, memory, skills, and projects). This covers the default copilot folder, your current Copilot folder if you changed it in Settings → Copilot → Basic → Copilot folder location, and every folder that has previously been your Copilot folder. Past Copilot folders stay excluded permanently, so any files the plugin left behind after a folder change never leak into search results.
Inclusions
Settings → Copilot → QA → Inclusions
Comma-separated list. If set, only notes matching these patterns are indexed. Useful for indexing a specific area of your vault.
Leave empty to include everything (except exclusions).
Embedding Settings
These settings appear in Settings → Copilot → QA when Semantic Search is enabled.
Requests per Minute
How many embedding API requests to send per minute. Default is 60. Decrease this if you hit rate limit errors from your embedding provider.
Range: 10–60
Embedding Batch Size
How many text chunks to send per API request. Default is 16. Larger batches are faster but may cause issues with some providers.
Partitions
The index is split into partitions to handle large vaults. You can control the number of partitions in Settings → Copilot → QA → Number of Partitions. If you have a large vault, increase this value to avoid index errors.
If you hit a "RangeError: invalid string length" error: This means your vault is too large for a single partition. Increase the number of partitions in QA settings. A good rule of thumb is that the first partition file (found in
.obsidian/) should be under ~400 MB.
Inline Citations (Experimental)
When enabled, AI responses in Vault QA include footnote-style citations pointing to the source notes used in the answer.
Enable: Settings → Copilot → QA → Enable Inline Citations
This is an experimental feature. Not all models handle it well.
Obsidian Sync
If you use Obsidian Sync, the vector index can be synced across devices. Enable Settings → Copilot → QA → Enable Index Sync.
Note: The index can be large (hundreds of MB for big vaults). Keep this in mind for sync limits and mobile data usage.
Mobile Considerations
By default, Copilot disables indexing on mobile to save battery and data. The setting is in Settings → Copilot → QA → Disable index on mobile (on by default).
On mobile, you can still use Vault QA with lexical search, but semantic search won't update automatically.
Related
- Agent Mode and Tools — How coding agents work with vault and web evidence
- Paid Plans and Self-Host — Miyo-powered local semantic search