This is my vault. I didn't draw any of it.

For about two years my note practice was really two practices wearing one name. One of them was reading and thinking. The other was bookkeeping: remembering that the note I'm writing now touches something I wrote in March, going to find it, linking it, tagging it, filing it. I told myself the bookkeeping was the thinking. It isn't unfortunately. It's clerical work with a very good disguise, and it eats the same attention that reading needs.

So I handed the mechanical half over. The connections in this graph were proposed mechanically: every note gets compared against every other note on the words it actually uses, links get written where a note names something the vault already has, and the colours are communities the graph found on its own, each one labelled with the words that cluster has and its neighbours don't. Nothing here was a model or an API. It's counting words and comparing sets, which is why it's fast and why it's honest about what it doesn't know.

What I did not expect is that having it built for me changed what I could see and finally learn.

When you link by hand you only ever see one edge at a time, the one you're currently making. You never get the whole shape, because you're inside it. Getting the whole thing at once, already connected, meant the first question stopped being "what should I link this to" and became "why is that over there" or "why are these two correlated".

The order of operations flipped, is what really happened. I used to think you connect notes and then the structure emerges later, if you're diligent. And that's true! But what if the structure arrives first, mechanically, and I read it and then edit the notes into better, more personal shape? The wrong edges are useful too. When it insists two notes are about the same thing and I'm sure they aren't, one of them is usually vague, and that's my problem, not the algorithm's. I've rewritten more notes because of a connection I disagreed with than because of one I liked.

Two things I'd want to know if I were reading this post instead of writing it. It proposes; it doesn't rearrange your vault behind your back. The only thing that writes is the autolink pass, and every write goes into a changes list with a per-file diff so you look at it and revert what you don't want. And it runs entirely on your machine with no network at all, which for me was the whole point, since a vault is the least appropriate thing I own to hand to somebody else's server.

I'm still figuring out how often to regenerate it. Every time I look, the seams have moved a little.

Thanks for reading this far. You can try it on a messy vault rather than a clean one, that's where it has something to say.

Repo: https://github.com/kiycoh/silica-agent

Hi everyone!!

I'd like to present my first Obsidian plugin after near 5+ years of using this fantastic app. My vault got past the size where I can keep it in my head. Backlinks answer "who linked here", and linking is precisely the thing I forgot to do.

So I wrote Silica Bridge. It's a panel that tells you more about your vault, and what your vault already knows about the note you have open (considering all of them!). No LLM model, no network, no configuration. The index is built from your notes, lives in memory, never touches disk, and a rebuild only re-reads the files whose mtime moved.

And It's completely free.

What the panel says about the current note, each note listed once under the sharpest thing there is to say about it:

- Related: notes that share vocabulary with this one, whether or not anyone ever linked them. A row marked `unlinked` is one where the overlap clears the bar and no wikilink exists in either direction. This is the feature I actually wanted.

- Near-duplicates: the same idea captured twice. Different metric from Related, so two notes on one subject don't read as copies of each other.

- Orphans you could adopt: notes nothing points at that overlap this one. An orphan is invisible from itself, because you never open it. This is the only surface where one can show up.

- Links without substance: links written out of this note whose target shares almost no vocabulary with it. Index notes are exempt.

- Broken links.

There's a Next button at the top that walks the entire vault worst-first, one note per press, and tells you why each one is there. Nothing is remembered between presses. The signal is the state, so a note you fix simply stops qualifying and you never maintain a queue.

Search that ranks. BM25 fused with a title match. Obsidian's own search is a boolean filter where every hit is equally good; this one puts the best one first, with a line of context and the match highlighted. Put `path:folder/` anywhere in the query to scope it.

Autolink this note, or autolink every note. It injects wikilinks for vault titles a note mentions but doesn't link, skipping frontmatter, code, math, headings and existing links. Every write lands in a source-control-style changes list with a per-file diff, so you look at what it did and revert file by file before keeping any of it. Autolink is the only thing here that writes to your vault, and only when you ask.

Community graph. Louvain over your written links plus the inferred ones, one hue per community, each labelled with the words that community has and its neighbours don't.

A note on daily notes, because that's what usually breaks this kind of tool. A vault built from one template shares its scaffolding across every file, so a naive overlap decides all of them are related to all of them. Every proposal here is gated on the overlap that survives dropping the words more than a quarter of the vault carries. That kills the whole class inside the algorithm, which is why there's no list of dismissed suggestions for you to babysit.

Thanks for reading this far. You can try it on a messy vault rather than a clean one, that's where it has something to say.

Install the community plugin,via the official Obsidian marketplace, enter `silica brige`, enable Silica Bridge, open a note and hit the ribbon icon.

Repo: https://github.com/kiycoh/obsidian-silica (MIT)

Hi everyone,

If you manage a large knowledge base, or big doc folders for your project you know the friction of distilling dozens of papers, legal docs, books, web searches. It's a massive manual bottleneck before actual learning happens, and usually the final docs will be forgotten once you've used it, even though it might come in handy in the future.

Dumping 40 files into a 1M context window isn't the solution tho. Models return incomplete summaries, drop edge cases, and give zero visibility into what they missed ( https://arxiv.org/abs/2509.04664 ). On top of that, standard AI tools and PKM plugins are notoriously risky: they overwrite notes, mangle frontmatter, break wikilinks, and corrupt vault architecture. ( https://arxiv.org/abs/2604.15597 )

I built Silica to solve this: an open-source agentic CLI that processes heavy document batches into clean, atomic Markdown notes while keeping your vault completely safe.

Why not just using using another knowledge manager or a memory agent?

Silica differs greatly from traditional note-taking skills and memory tools because it's an agent that views your notes not simply as text to be read, but as its knowledge base (not graph, but it benefits from it). In Silica, memory and knowledge are closely related but still distinct.

- For example Silica keeps track of the conversations you've already had with Claude or ChatGPT, automatically linking them to the relative documentation in your repository, automatically.

- Silica can also links concepts from multiple books/papers/notes sparse in your folder automatically, if they share something maybe you didn't see.

- It can "digest" large quantities of files, coherently, and safely (without causing corruption, in a different folder from the vault root).

These aren't even its most notable features, but rather a byproduct of its architectural design. There is still considerable room for improvement. This is a broad project.

What Silica does

• Batch Atomic Distillation: Feed 20-30 documents or full (multiple) books in a single command. Silica extracts core concepts into atomic notes (one note per idea), links them via wikilinks, and files them logically.
• Stateful Continuity: What a model can't process in one go gets written out statefully. The next execution picks up from the saved state instead of starting over.
• The source of a note is always provided: A section is added to the frontmatter that indicates where the note was extracted or converted from, so that you always have a reference to the original document.

Why your vault is finally safe

Most AI integration tools treat your vault like a loose text buffer. Silica treats it like a transactional database with strict guardrails:

• SAFE MODE (Isolated Staging): You can execute ingestion in a dedicated staging folder/container. Notes are written in isolation first so you can inspect, verify, and merge them only when you trust the output.
• Write Verification: Every write operation is re-read post-commit. If syntax, formatting, or links broke, it automatically rolls back.
• Wikilink Refactoring: If a note is moved during organization, all wikilinks across your vault referencing it are dynamically updated to prevent broken links.
• Full Rollback Control: Complete transaction safety with /undo (single note) and /revert (entire session batch). Nothing enters your main graph permanently without your control.

Grounded Retrieval & Graph Exploration

• Zero-Hallucination Fallback: Uses local semantic search. If your knowledge base doesn't contain the answer to a query, Silica explicitly tells you instead of hallucinating.
• Graph Mapping: Explore concept connections visually to discover implicit links across unrelated documents.

Silica isn't built to replace human learning, it eliminates the operational overhead of structuring and formatting raw data. Works via TUI, GUI, MCP, Obsidian Plugin ( https://github.com/kiycoh/obsidian-silica )

GitHub Repository: https://github.com/kiycoh/silica-agent (~1000 commits as solo dev)

I'd love to hear your feedback, workflow suggestions, or technical thoughts!

Hi everyone,

If you manage a large knowledge base, or big doc folders for your project you know the friction of distilling dozens of papers, legal docs, books, web searches. It's a massive manual bottleneck before actual learning happens, and usually the final docs will be forgotten once you've used it, even though it might come in handy in the future.

Dumping 40 files into a 1M context window isn't the solution tho. Models return incomplete summaries, drop edge cases, and give zero visibility into what they missed ( https://arxiv.org/abs/2509.04664 ). On top of that, standard AI tools and PKM plugins are notoriously risky: they overwrite notes, mangle frontmatter, break wikilinks, and corrupt vault architecture. ( https://arxiv.org/abs/2604.15597 )

I built Silica to solve this: an open-source agentic CLI that processes heavy document batches into clean, atomic Markdown notes while keeping your vault completely safe.

Why not just using using another knowledge manager or a memory agent?

Silica differs greatly from traditional note-taking skills and memory tools because it's an agent that views your notes not simply as text to be read, but as its knowledge base (not graph, but it benefits from it). In Silica, memory and knowledge are closely related but still distinct.

- For example Silica keeps track of the conversations you've already had with Claude or ChatGPT, automatically linking them to the relative documentation in your repository, automatically.

- Silica can also links concepts from multiple books/papers/notes sparse in your folder automatically, if they share something maybe you didn't see.

- It can "digest" large quantities of files, coherently, and safely (without causing corruption, in a different folder from the vault root).

These aren't even its most notable features, but rather a byproduct of its architectural design. There is still considerable room for improvement. This is a broad project.

What Silica does

• Batch Atomic Distillation: Feed 20-30 documents or full (multiple) books in a single command. Silica extracts core concepts into atomic notes (one note per idea), links them via wikilinks, and files them logically.
• Stateful Continuity: What a model can't process in one go gets written out statefully. The next execution picks up from the saved state instead of starting over.
• The source of a note is always provided: A section is added to the frontmatter that indicates where the note was extracted or converted from, so that you always have a reference to the original document.

Why your vault is finally safe

Most AI integration tools treat your vault like a loose text buffer. Silica treats it like a transactional database with strict guardrails:

• SAFE MODE (Isolated Staging): You can execute ingestion in a dedicated staging folder/container. Notes are written in isolation first so you can inspect, verify, and merge them only when you trust the output.
• Write Verification: Every write operation is re-read post-commit. If syntax, formatting, or links broke, it automatically rolls back.
• Wikilink Refactoring: If a note is moved during organization, all wikilinks across your vault referencing it are dynamically updated to prevent broken links.
• Full Rollback Control: Complete transaction safety with /undo (single note) and /revert (entire session batch). Nothing enters your main graph permanently without your control.

Grounded Retrieval & Graph Exploration

• Zero-Hallucination Fallback: Uses local semantic search. If your knowledge base doesn't contain the answer to a query, Silica explicitly tells you instead of hallucinating.
• Graph Mapping: Explore concept connections visually to discover implicit links across unrelated documents.

Silica isn't built to replace human learning, it eliminates the operational overhead of structuring and formatting raw data. Works via TUI, GUI, MCP, Obsidian Plugin ( https://github.com/kiycoh/obsidian-silica )

GitHub Repository: https://github.com/kiycoh/silica-agent (~1000 commits as solo dev)

I'd love to hear your feedback, workflow suggestions, or technical thoughts!

Hi everyone,

If you manage a large knowledge base, or big doc folders for your project you know the friction of distilling dozens of papers, legal docs, books, web searches. It's a massive manual bottleneck before actual learning happens, and usually the final docs will be forgotten once you've used it, even though it might come in handy in the future.

Dumping 40 files into a 1M context window isn't the solution tho. Models return incomplete summaries, drop edge cases, and give zero visibility into what they missed ( https://arxiv.org/abs/2509.04664 ). On top of that, standard AI tools and PKM plugins are notoriously risky: they overwrite notes, mangle frontmatter, break wikilinks, and corrupt vault architecture. ( https://arxiv.org/abs/2604.15597 )

I built Silica to solve this: an open-source agentic CLI that processes heavy document batches into clean, atomic Markdown notes while keeping your vault completely safe.

Why not just using using another knowledge manager or a memory agent?

Silica differs greatly from traditional note-taking skills and memory tools because it's an agent that views your notes not simply as text to be read, but as its knowledge base (not graph, but it benefits from it). In Silica, memory and knowledge are closely related but still distinct.

- For example Silica keeps track of the conversations you've already had with Claude or ChatGPT, automatically linking them to the relative documentation in your repository, automatically.

- Silica can also links concepts from multiple books/papers/notes sparse in your folder automatically, if they share something maybe you didn't see.

- It can "digest" large quantities of files, coherently, and safely (without causing corruption, in a different folder from the vault root).

These aren't even its most notable features, but rather a byproduct of its architectural design. There is still considerable room for improvement. This is a broad project.

What Silica does

• Batch Atomic Distillation: Feed 20-30 documents or full (multiple) books in a single command. Silica extracts core concepts into atomic notes (one note per idea), links them via wikilinks, and files them logically.
• Stateful Continuity: What a model can't process in one go gets written out statefully. The next execution picks up from the saved state instead of starting over.
• The source of a note is always provided: A section is added to the frontmatter that indicates where the note was extracted or converted from, so that you always have a reference to the original document.

Why your vault is finally safe

Most AI integration tools treat your vault like a loose text buffer. Silica treats it like a transactional database with strict guardrails:

• SAFE MODE (Isolated Staging): You can execute ingestion in a dedicated staging folder/container. Notes are written in isolation first so you can inspect, verify, and merge them only when you trust the output.
• Write Verification: Every write operation is re-read post-commit. If syntax, formatting, or links broke, it automatically rolls back.
• Wikilink Refactoring: If a note is moved during organization, all wikilinks across your vault referencing it are dynamically updated to prevent broken links.
• Full Rollback Control: Complete transaction safety with /undo (single note) and /revert (entire session batch). Nothing enters your main graph permanently without your control.

Grounded Retrieval & Graph Exploration

• Zero-Hallucination Fallback: Uses local semantic search. If your knowledge base doesn't contain the answer to a query, Silica explicitly tells you instead of hallucinating.
• Graph Mapping: Explore concept connections visually to discover implicit links across unrelated documents.

Silica isn't built to replace human learning, it eliminates the operational overhead of structuring and formatting raw data. Works via TUI, GUI, MCP, Obsidian Plugin ( https://github.com/kiycoh/obsidian-silica )

GitHub Repository: https://github.com/kiycoh/silica-agent (~1000 commits as solo dev)

I'd love to hear your feedback, workflow suggestions, or technical thoughts!

Hi everyone,

If you manage a large knowledge base, or big doc folders for your project you know the friction of distilling dozens of papers, legal docs, books, web searches. It's a massive manual bottleneck before actual learning happens, and usually the final docs will be forgotten once you've used it, even though it might come in handy in the future.

Dumping 40 files into a 1M context window isn't the solution tho. Models return incomplete summaries, drop edge cases, and give zero visibility into what they missed ( https://arxiv.org/abs/2509.04664 ). On top of that, standard AI tools and PKM plugins are notoriously risky: they overwrite notes, mangle frontmatter, break wikilinks, and corrupt vault architecture. ( https://arxiv.org/abs/2604.15597 )

I built Silica to solve this: an open-source agentic CLI that processes heavy document batches into clean, atomic Markdown notes while keeping your vault completely safe.

Why not just using using another knowledge manager or a memory agent?

Silica differs greatly from traditional note-taking skills and memory tools because it's an agent that views your notes not simply as text to be read, but as its knowledge base (not graph, but it benefits from it). In Silica, memory and knowledge are closely related but still distinct.

- For example Silica keeps track of the conversations you've already had with Claude or ChatGPT, automatically linking them to the relative documentation in your repository, automatically.

- Silica can also links concepts from multiple books/papers/notes sparse in your folder automatically, if they share something maybe you didn't see.

- It can "digest" large quantities of files, coherently, and safely (without causing corruption, in a different folder from the vault root).

These aren't even its most notable features, but rather a byproduct of its architectural design. There is still considerable room for improvement. This is a broad project.

What Silica does

• Batch Atomic Distillation: Feed 20-30 documents or full (multiple) books in a single command. Silica extracts core concepts into atomic notes (one note per idea), links them via wikilinks, and files them logically.
• Stateful Continuity: What a model can't process in one go gets written out statefully. The next execution picks up from the saved state instead of starting over.
• The source of a note is always provided: A section is added to the frontmatter that indicates where the note was extracted or converted from, so that you always have a reference to the original document.

Why your vault is finally safe

Most AI integration tools treat your vault like a loose text buffer. Silica treats it like a transactional database with strict guardrails:

• SAFE MODE (Isolated Staging): You can execute ingestion in a dedicated staging folder/container. Notes are written in isolation first so you can inspect, verify, and merge them only when you trust the output.
• Write Verification: Every write operation is re-read post-commit. If syntax, formatting, or links broke, it automatically rolls back.
• Wikilink Refactoring: If a note is moved during organization, all wikilinks across your vault referencing it are dynamically updated to prevent broken links.
• Full Rollback Control: Complete transaction safety with /undo (single note) and /revert (entire session batch). Nothing enters your main graph permanently without your control.

Grounded Retrieval & Graph Exploration

• Zero-Hallucination Fallback: Uses local semantic search. If your knowledge base doesn't contain the answer to a query, Silica explicitly tells you instead of hallucinating.
• Graph Mapping: Explore concept connections visually to discover implicit links across unrelated documents.

Silica isn't built to replace human learning, it eliminates the operational overhead of structuring and formatting raw data. Works via TUI, GUI, MCP, Obsidian Plugin ( https://github.com/kiycoh/obsidian-silica )

GitHub Repository: https://github.com/kiycoh/silica-agent (~1000 commits as solo dev)

I'd love to hear your feedback, workflow suggestions, or technical thoughts!

Hi everyone,

If you manage a large knowledge base, or big doc folders for your project you know the friction of distilling dozens of papers, legal docs, books, web searches. It's a massive manual bottleneck before actual learning happens, and usually the final docs will be forgotten once you've used it, even though it might come in handy in the future.

Dumping 40 files into a 1M context window isn't the solution tho. Models return incomplete summaries, drop edge cases, and give zero visibility into what they missed ( https://arxiv.org/abs/2509.04664 ). On top of that, standard AI tools and PKM plugins are notoriously risky: they overwrite notes, mangle frontmatter, break wikilinks, and corrupt vault architecture. ( https://arxiv.org/abs/2604.15597 )

I built Silica to solve this: an open-source agentic CLI that processes heavy document batches into clean, atomic Markdown notes while keeping your vault completely safe.

Why not just using using another knowledge manager or a memory agent?

Silica differs greatly from traditional note-taking skills and memory tools because it's an agent that views your notes not simply as text to be read, but as its knowledge base (not graph, but it benefits from it). In Silica, memory and knowledge are closely related but still distinct.

- For example Silica keeps track of the conversations you've already had with Claude or ChatGPT, automatically linking them to the relative documentation in your repository, automatically.

- Silica can also links concepts from multiple books/papers/notes sparse in your folder automatically, if they share something maybe you didn't see.

- It can "digest" large quantities of files, coherently, and safely (without causing corruption, in a different folder from the vault root).

These aren't even its most notable features, but rather a byproduct of its architectural design. There is still considerable room for improvement. This is a broad project.

What Silica does

• Batch Atomic Distillation: Feed 20-30 documents or full (multiple) books in a single command. Silica extracts core concepts into atomic notes (one note per idea), links them via wikilinks, and files them logically.
• Stateful Continuity: What a model can't process in one go gets written out statefully. The next execution picks up from the saved state instead of starting over.
• The source of a note is always provided: A section is added to the frontmatter that indicates where the note was extracted or converted from, so that you always have a reference to the original document.

Why your vault is finally safe

Most AI integration tools treat your vault like a loose text buffer. Silica treats it like a transactional database with strict guardrails:

• SAFE MODE (Isolated Staging): You can execute ingestion in a dedicated staging folder/container. Notes are written in isolation first so you can inspect, verify, and merge them only when you trust the output.
• Write Verification: Every write operation is re-read post-commit. If syntax, formatting, or links broke, it automatically rolls back.
• Wikilink Refactoring: If a note is moved during organization, all wikilinks across your vault referencing it are dynamically updated to prevent broken links.
• Full Rollback Control: Complete transaction safety with /undo (single note) and /revert (entire session batch). Nothing enters your main graph permanently without your control.

Grounded Retrieval & Graph Exploration

• Zero-Hallucination Fallback: Uses local semantic search. If your knowledge base doesn't contain the answer to a query, Silica explicitly tells you instead of hallucinating.
• Graph Mapping: Explore concept connections visually to discover implicit links across unrelated documents.

Silica isn't built to replace human learning, it eliminates the operational overhead of structuring and formatting raw data. Works via TUI, GUI, MCP, Obsidian Plugin ( https://github.com/kiycoh/obsidian-silica )

GitHub Repository: https://github.com/kiycoh/silica-agent (~1000 commits as solo dev)

I'd love to hear your feedback, workflow suggestions, or technical thoughts!

Hi everyone,

If you manage a large knowledge base, or big doc folders for your project you know the friction of distilling dozens of papers, legal docs, books, web searches. It's a massive manual bottleneck before actual learning happens, and usually the final docs will be forgotten once you've used it, even though it might come in handy in the future.

Dumping 40 files into a 1M context window isn't the solution tho. Models return incomplete summaries, drop edge cases, and give zero visibility into what they missed ( https://arxiv.org/abs/2509.04664 ). On top of that, standard AI tools and PKM plugins are notoriously risky: they overwrite notes, mangle frontmatter, break wikilinks, and corrupt vault architecture. ( https://arxiv.org/abs/2604.15597 )

I built Silica to solve this: an open-source agentic CLI that processes heavy document batches into clean, atomic Markdown notes while keeping your vault completely safe.

Why not just using using another knowledge manager or a memory agent?

Silica differs greatly from traditional note-taking skills and memory tools because it's an agent that views your notes not simply as text to be read, but as its knowledge base (not graph, but it benefits from it). In Silica, memory and knowledge are closely related but still distinct.

- For example Silica keeps track of the conversations you've already had with Claude or ChatGPT, automatically linking them to the relative documentation in your repository, automatically.

- Silica can also links concepts from multiple books/papers/notes sparse in your folder automatically, if they share something maybe you didn't see.

- It can "digest" large quantities of files, coherently, and safely (without causing corruption, in a different folder from the vault root).

These aren't even its most notable features, but rather a byproduct of its architectural design. There is still considerable room for improvement. This is a broad project.

What Silica does

• Batch Atomic Distillation: Feed 20-30 documents or full (multiple) books in a single command. Silica extracts core concepts into atomic notes (one note per idea), links them via wikilinks, and files them logically.
• Stateful Continuity: What a model can't process in one go gets written out statefully. The next execution picks up from the saved state instead of starting over.
• The source of a note is always provided: A section is added to the frontmatter that indicates where the note was extracted or converted from, so that you always have a reference to the original document.

Why your vault is finally safe

Most AI integration tools treat your vault like a loose text buffer. Silica treats it like a transactional database with strict guardrails:

• SAFE MODE (Isolated Staging): You can execute ingestion in a dedicated staging folder/container. Notes are written in isolation first so you can inspect, verify, and merge them only when you trust the output.
• Write Verification: Every write operation is re-read post-commit. If syntax, formatting, or links broke, it automatically rolls back.
• Wikilink Refactoring: If a note is moved during organization, all wikilinks across your vault referencing it are dynamically updated to prevent broken links.
• Full Rollback Control: Complete transaction safety with /undo (single note) and /revert (entire session batch). Nothing enters your main graph permanently without your control.

Grounded Retrieval & Graph Exploration

• Zero-Hallucination Fallback: Uses local semantic search. If your knowledge base doesn't contain the answer to a query, Silica explicitly tells you instead of hallucinating.
• Graph Mapping: Explore concept connections visually to discover implicit links across unrelated documents.

Silica isn't built to replace human learning, it eliminates the operational overhead of structuring and formatting raw data. Works via TUI, GUI, MCP, Obsidian Plugin ( https://github.com/kiycoh/obsidian-silica )

GitHub Repository: https://github.com/kiycoh/silica-agent (~1000 commits as solo dev)

I'd love to hear your feedback, workflow suggestions, or technical thoughts!

Hi everyone,

If you manage a large knowledge base, or big doc folders for your project you know the friction of distilling dozens of papers, legal docs, books, web searches. It's a massive manual bottleneck before actual learning happens, and usually the final docs will be forgotten once you've used it, even though it might come in handy in the future.

Dumping 40 files into a 1M context window isn't the solution tho. Models return incomplete summaries, drop edge cases, and give zero visibility into what they missed ( https://arxiv.org/abs/2509.04664 ). On top of that, standard AI tools and PKM plugins are notoriously risky: they overwrite notes, mangle frontmatter, break wikilinks, and corrupt vault architecture. ( https://arxiv.org/abs/2604.15597 )

I built Silica to solve this: an open-source agentic CLI that processes heavy document batches into clean, atomic Markdown notes while keeping your vault completely safe.

Why not just using using another knowledge manager or a memory agent?

Silica differs greatly from traditional note-taking skills and memory tools because it's an agent that views your notes not simply as text to be read, but as its knowledge base (not graph, but it benefits from it). In Silica, memory and knowledge are closely related but still distinct.

- For example Silica keeps track of the conversations you've already had with Claude or ChatGPT, automatically linking them to the relative documentation in your repository, automatically.

- Silica can also links concepts from multiple books/papers/notes sparse in your folder automatically, if they share something maybe you didn't see.

- It can "digest" large quantities of files, coherently, and safely (without causing corruption, in a different folder from the vault root).

These aren't even its most notable features, but rather a byproduct of its architectural design. There is still considerable room for improvement. This is a broad project.

What Silica does

• Batch Atomic Distillation: Feed 20-30 documents or full (multiple) books in a single command. Silica extracts core concepts into atomic notes (one note per idea), links them via wikilinks, and files them logically.
• Stateful Continuity: What a model can't process in one go gets written out statefully. The next execution picks up from the saved state instead of starting over.
• The source of a note is always provided: A section is added to the frontmatter that indicates where the note was extracted or converted from, so that you always have a reference to the original document.

Why your vault is finally safe

Most AI integration tools treat your vault like a loose text buffer. Silica treats it like a transactional database with strict guardrails:

• SAFE MODE (Isolated Staging): You can execute ingestion in a dedicated staging folder/container. Notes are written in isolation first so you can inspect, verify, and merge them only when you trust the output.
• Write Verification: Every write operation is re-read post-commit. If syntax, formatting, or links broke, it automatically rolls back.
• Wikilink Refactoring: If a note is moved during organization, all wikilinks across your vault referencing it are dynamically updated to prevent broken links.
• Full Rollback Control: Complete transaction safety with /undo (single note) and /revert (entire session batch). Nothing enters your main graph permanently without your control.

Grounded Retrieval & Graph Exploration

• Zero-Hallucination Fallback: Uses local semantic search. If your knowledge base doesn't contain the answer to a query, Silica explicitly tells you instead of hallucinating.
• Graph Mapping: Explore concept connections visually to discover implicit links across unrelated documents.

Silica isn't built to replace human learning, it eliminates the operational overhead of structuring and formatting raw data. Works via TUI, GUI, MCP, Obsidian Plugin ( https://github.com/kiycoh/obsidian-silica )

GitHub Repository: https://github.com/kiycoh/silica-agent (~1000 commits as solo dev)

I'd love to hear your feedback, workflow suggestions, or technical thoughts!

Hi everyone,

If you manage a large knowledge base, or big doc folders for your project you know the friction of distilling dozens of papers, legal docs, books, web searches. It's a massive manual bottleneck before actual learning happens, and usually the final docs will be forgotten once you've used it, even though it might come in handy in the future.

Dumping 40 files into a 1M context window isn't the solution tho. Models return incomplete summaries, drop edge cases, and give zero visibility into what they missed ( https://arxiv.org/abs/2509.04664 ). On top of that, standard AI tools and PKM plugins are notoriously risky: they overwrite notes, mangle frontmatter, break wikilinks, and corrupt vault architecture. ( https://arxiv.org/abs/2604.15597 )

I built Silica to solve this: an open-source agentic CLI that processes heavy document batches into clean, atomic Markdown notes while keeping your vault completely safe.

Why not just using using another knowledge manager or a memory agent?

Silica differs greatly from traditional note-taking skills and memory tools because it's an agent that views your notes not simply as text to be read, but as its knowledge base (not graph, but it benefits from it). In Silica, memory and knowledge are closely related but still distinct.

- For example Silica keeps track of the conversations you've already had with Claude or ChatGPT, automatically linking them to the relative documentation in your repository, automatically.

- Silica can also links concepts from multiple books/papers/notes sparse in your folder automatically, if they share something maybe you didn't see.

- It can "digest" large quantities of files, coherently, and safely (without causing corruption, in a different folder from the vault root).

These aren't even its most notable features, but rather a byproduct of its architectural design. There is still considerable room for improvement. This is a broad project.

What Silica does

• Batch Atomic Distillation: Feed 20-30 documents or full (multiple) books in a single command. Silica extracts core concepts into atomic notes (one note per idea), links them via wikilinks, and files them logically.
• Stateful Continuity: What a model can't process in one go gets written out statefully. The next execution picks up from the saved state instead of starting over.
• The source of a note is always provided: A section is added to the frontmatter that indicates where the note was extracted or converted from, so that you always have a reference to the original document.

Why your vault is finally safe

Most AI integration tools treat your vault like a loose text buffer. Silica treats it like a transactional database with strict guardrails:

• SAFE MODE (Isolated Staging): You can execute ingestion in a dedicated staging folder/container. Notes are written in isolation first so you can inspect, verify, and merge them only when you trust the output.
• Write Verification: Every write operation is re-read post-commit. If syntax, formatting, or links broke, it automatically rolls back.
• Wikilink Refactoring: If a note is moved during organization, all wikilinks across your vault referencing it are dynamically updated to prevent broken links.
• Full Rollback Control: Complete transaction safety with /undo (single note) and /revert (entire session batch). Nothing enters your main graph permanently without your control.

Grounded Retrieval & Graph Exploration

• Zero-Hallucination Fallback: Uses local semantic search. If your knowledge base doesn't contain the answer to a query, Silica explicitly tells you instead of hallucinating.
• Graph Mapping: Explore concept connections visually to discover implicit links across unrelated documents.

Silica isn't built to replace human learning, it eliminates the operational overhead of structuring and formatting raw data. Works via TUI, GUI, MCP, Obsidian Plugin ( https://github.com/kiycoh/obsidian-silica )

GitHub Repository: https://github.com/kiycoh/silica-agent (~1000 commits as solo dev)

I'd love to hear your feedback, workflow suggestions, or technical thoughts!

Hi everyone,

If you manage a large knowledge base, or big doc folders for your project you know the friction of distilling dozens of papers, legal docs, books, web searches. It's a massive manual bottleneck before actual learning happens, and usually the final docs will be forgotten once you've used it, even though it might come in handy in the future.

Dumping 40 files into a 1M context window isn't the solution tho. Models return incomplete summaries, drop edge cases, and give zero visibility into what they missed ( https://arxiv.org/abs/2509.04664 ). On top of that, standard AI tools and PKM plugins are notoriously risky: they overwrite notes, mangle frontmatter, break wikilinks, and corrupt vault architecture. ( https://arxiv.org/abs/2604.15597 )

I built Silica to solve this: an open-source agentic CLI that processes heavy document batches into clean, atomic Markdown notes while keeping your vault completely safe.

Why not just using using another knowledge manager or a memory agent?

Silica differs greatly from traditional note-taking skills and memory tools because it's an agent that views your notes not simply as text to be read, but as its knowledge base (not graph, but it benefits from it). In Silica, memory and knowledge are closely related but still distinct.

- For example Silica keeps track of the conversations you've already had with Claude or ChatGPT, automatically linking them to the relative documentation in your repository, automatically.

- Silica can also links concepts from multiple books/papers/notes sparse in your folder automatically, if they share something maybe you didn't see.

- It can "digest" large quantities of files, coherently, and safely (without causing corruption, in a different folder from the vault root).

These aren't even its most notable features, but rather a byproduct of its architectural design. There is still considerable room for improvement. This is a broad project.

What Silica does

• Batch Atomic Distillation: Feed 20-30 documents or full (multiple) books in a single command. Silica extracts core concepts into atomic notes (one note per idea), links them via wikilinks, and files them logically.
• Stateful Continuity: What a model can't process in one go gets written out statefully. The next execution picks up from the saved state instead of starting over.
• The source of a note is always provided: A section is added to the frontmatter that indicates where the note was extracted or converted from, so that you always have a reference to the original document.

Why your vault is finally safe

Most AI integration tools treat your vault like a loose text buffer. Silica treats it like a transactional database with strict guardrails:

• SAFE MODE (Isolated Staging): You can execute ingestion in a dedicated staging folder/container. Notes are written in isolation first so you can inspect, verify, and merge them only when you trust the output.
• Write Verification: Every write operation is re-read post-commit. If syntax, formatting, or links broke, it automatically rolls back.
• Wikilink Refactoring: If a note is moved during organization, all wikilinks across your vault referencing it are dynamically updated to prevent broken links.
• Full Rollback Control: Complete transaction safety with /undo (single note) and /revert (entire session batch). Nothing enters your main graph permanently without your control.

Grounded Retrieval & Graph Exploration

• Zero-Hallucination Fallback: Uses local semantic search. If your knowledge base doesn't contain the answer to a query, Silica explicitly tells you instead of hallucinating.
• Graph Mapping: Explore concept connections visually to discover implicit links across unrelated documents.

Silica isn't built to replace human learning, it eliminates the operational overhead of structuring and formatting raw data. Works via TUI, GUI, MCP, Obsidian Plugin ( https://github.com/kiycoh/obsidian-silica )

GitHub Repository: https://github.com/kiycoh/silica-agent (~1000 commits as solo dev)

I'd love to hear your feedback, workflow suggestions, or technical thoughts!

"I let an assistant edit my notes for a few weeks. It went fine, I guessed, which is the problem."

Some of the problems i found: links pointing at files that no longer existed, one idea saved four separate times under four titles, ephemeral things explained too deeply. rip vault.

Why this happens

1. The model is worst exactly where your notes live.

>"Why Language Models Hallucinate" (Kalai et al., 2025, arXiv:2509.04664 - https://arxiv.org/abs/2509.04664 ) shows that hallucination is not a defect that gets trained away. It has a floor, and the floor is highest for facts that were never in the training data.

2. Long editing sessions corrupt documents, silently.

>"LLMs Corrupt Your Documents When You Delegate" (Laban et al., 2026, arXiv:2604.15597 - https://arxiv.org/abs/2604.15597 ) ran models through long document editing workflows. Roughly a quarter of documents came out corrupted, frontier models included.

Two workarounds that did not fix it.

- Keep the assistant read only. Then nothing gets corrupted, but the folder rots on its own anyway: duplicates, orphans, dead links, a page describing how something worked three months ago.

- Use a memory tool. Most of them ingest your notes into a store of their own, a vector index or a graph database. Now the corpus that is being corrupted is one you cannot open in a text editor to check.

What already works (I really took it for granted).

You already let a model write into your code. It is not because the model is trustworthy. It is because nothing lands unchecked. The compiler rejects what will not build etc.. Git rolls back a bad commit.

Markdown files never got that layer. So build it:

- The model proposes a change. It does not write.

- A parser and a state machine check the proposal against structural rules and either execute it or reject it.

- After the write lands, the file is read back and compared to what was supposed to be there.

- Renames and merges redirect the links that pointed at the old note, so a reorganize never leaves an orphan.

- Undo per note, revert per whole run, and optionally a git commit per write.

Silica ( github.com/kiycoh/silica-agent ) is a proof of concept, AGPL, it runs locally, and it works on a plain folder of .md files that stays readable with or without it. It ships a graph view, retrieval that still works with no embedding model at all, and an MCP server so an assistant you already run can read your real notes.

It is based on Karpathy's LLM Wiki, which Google Cloud later formalized as the Open Knowledge Format. What I added is the gate in front of it.

I'd love to hear your thoughts about this.

>Not sped up. This is just how Silica works.

The idea is simple:

1. Drop. Clippings, drafts, PDFs, notebooks go in `Inbox/`. `/nucleate Inbox/*` distills each one into an atomic note, checks it against what you already have so you do not end up with a fifth copy of the same idea, and files it (it can ingest 10+ papers or multiple entire books in one run without losing details).

2.Curate. /curate autolinks and dedupes what is already there. /organize "<intent>" reclassifies by what you actually want rather than a fixed taxonomy. /report is read-only and just shows you the hubs, bridges and orphans you already have.

3. Undo. `/undo takes back the last edit to a note, `/revert` takes back a whole run, and an optional git commit per write sits under both. (Bonus: Obsidian plugin Silica-Bridge let you see changes in git diff style blocks)

And then ask it: /explain, /compare "A" "B", /quiz where what you missed comes back and what you knew does not.

Why I built it this way:

- It edits your existing notes, and that is the hard part. Most tools in this space are append-only, which is the safe choice and also means they can never fix the mess you already have. So the write path works like a compiler: the model proposes the edit, it is applied, read back, and rolled back unless the vault still checks out. A merge redirects every incoming wikilink so it cannot leave an orphan.

- Plain markdown, no database. Your folder is the database. If you stop using Silica tomorrow you still have exactly what you had, greppable and diffable.

- The core needs no model at all. Search runs down independent legs fused by rank: embeddings, a co-occurrence concept graph, and an optional BM25 leg. The last two need no embedder, so with the model server down retrieval degrades instead of failing.

- Any model. LiteLLM under it, so OpenRouter, Gemini, OpenAI, or fully local through LM Studio or Ollama, one config value.

That wires it into an assistant you already run, and from the next session it searches and reads your real notes. There is also a terminal REPL, a local web UI, and an Obsidian plugin bridge where every change lands in a panel with a per-file diff.

Repo: github.com/kiycoh/silica-agent (AGPL)

What I would genuinely like opinions on: everyone who has tried letting a model touch an existing vault seems to have quit and gone append-only. If you tried it, what broke, and was it the edits themselves or not being able to see what changed?

>In the first image the plugin is on the top right corner, searched for something; second image I requested to edit it: git diff style blocks with accept/reject buttons.

I mostly agree with the people here who say don't let an LLM near your notes. The threads asking how to review AI changes to a vault usually get "don't use one" as the top answer, and that is a reasonable default. I'm not trying to talk anyone out of it.

What I wanted was the version where I stay in the loop.

Reading needs no model and no API key. Search, recall and note reading run on the folder itself, over the wikilinks you already wrote, so it finds your orphans and your unresolved links with nothing configured. If you never turn a model on, that is the whole tool.

Writing is opt-in, and it's the part I actually spent the time on. Every change arrives in the note as a block with an accept and a reject button, one hunk at a time, so nothing gets kept because you didn't notice it. Behind that, every write goes through one code path, the note is re-read after the write lands, and a failed check rolls it back. Renames and merges redirect the incoming wikilinks so a merge can't orphan a note. Undo per note, revert per run, optional git commit per write.

The plugin opens a WebSocket to 127.0.0.1 and nowhere else, and what it's allowed to do to the vault is a fixed allowlist.

Things I should say without being asked. It's a client, so it needs the Python agent running on the same machine, which is a pip install and one command inside your vault.

The write guard isn't crash-verified: I enforce it on the normal path but I haven't shipped the harness that kills the process mid-write, so keep backups (still working on it). And I'm the author. AGPL, no paid tier, no cloud, no telemetry.

Silica Bridge in Obsidian Community Plugins. Agent at github.com/kiycoh/silica-agent

~1.4k notes. Last year I started running LLM passes over my inbox:

distill, split into atomic notes, link them back. It worked until it didn't. I ended up with four near-identical notes on the same concept, written weeks apart. A rename silently orphaned six backlinks. Two weeks later I couldn't tell which edits were made by myself..

The failure mode isn't that the model writes badly. It's that nothing sits between the model and the filesystem. A bad write lands and becomes indistinguishable from a good one three commits later.

For people with vaults bigger than mine:

- do you let anything automated write into the vault, or is it strictly read-only + manual paste?

- if you do let it write, what catches the mistakes? git? review? nothing?

- has anyone actually lost structure this way, or do I just have bad habits?

>(Disclosure: I'm building something in this space, so I'm biased. Not linking it, I want to know if the problem is real before I keep going.)