Cursor slows down when chat history, Composer database rows, and cache pile up on disk. .MD Brain does not offer one blunt delete button — you get a customized cleanup toolkit for every situation, only after intelligence is preserved in Cloud Brain. Customer .md files are never deleted.

Before Bloated Cursor history
  • Giant state.vscdb footprint
  • Hundreds of transcript files
  • Secrets or noise trapped in old chats
  • Higher Bog Down score
Bogged Down 78%
After Knowledge preserved · Cursor lean
  • Valuable knowledge lives in your .md codex via Smart Deposits and summaries
  • Cloud Brain retains excerpts, scores & Go-Back history
  • Protected chats stay — the rest can go
  • .MD versioned recovery — conduct a “Go-Back” anytime
Bogged Down 0%

Search → Read → Protect

Protect Cursor Chats

Bulk cleanup should never delete the threads you still need. Protect Cursor Chats lets you search every chat on this computer, open any one in the .MD Brain Chat Viewer to read it first, then toggle it ON so Auto-Clean Step 3 skips it. Synchronized excerpts and audit history remain in Cloud Brain even when the local chat is later cleaned.

Protect Cursor Chats — filter chats by title or keyword, open a chat in .MD Brain Chat Viewer, then toggle ON to protect it from cleanup
Search · open · protect Filter the list, click a row to review the full chat, then toggle ON — protected chats stay in Cursor when you run cleanup. Cloud excerpts survive local deletion.
  1. 1
    Search your chats

    Filter by title or keyword — every Cursor chat on this PC appears in All Results, newest first.

  2. 2
    Open & review

    Click any row to open the .MD Brain Chat Viewer — read curated excerpts and audit context before you decide.

  3. 3
    Toggle ON to protect

    Flip the switch ON for chats you want to keep locally. They move to Chats You Chose To Protect and survive Step 3 cleanup.

Chats you protect stay in Cursor’s local database until you change your mind. This picker is desktop-only. Your local chat can disappear without taking all of its useful history with it.

Surgical

Playbook

Surgically fix one chat.

Find a specific Cursor chat by title, keyword, pattern, or ID—then run a recipe built for that situation. Playbook can preserve safe knowledge with Smart .MD Deposits and Summary & Suggestions updates in the appropriate approved .MD, and remove only the unwanted chat content, without wiping your entire Cursor history.

Quick actions

Manual Clean

Quick targeted cleanup functions.

When you already know what you want, skip the guided path. One-click presets like After audit (recommended) and Maximum squeeze, plus individual actions: clear Cursor cache, refresh Bog Down stats, delete audit-flagged chats, clear logs, shrink the Composer database, and more. Mix and match checkboxes — preview the batch, confirm, then run.

Guided path

Auto-Clean

Full guided cleanup workflow.

A stepped operator console on the Windows Command Panel Cleanup tab. Step 1 Sync captures signal to Cloud Brain before cleanup continues. Step 2 Audit marks what is safe to clear. Step 2.5 Protect Cursor Chats (desktop-only, featured above) lets you search, review, and save the chats you need locally. Step 3 What to Clean runs only what you checked — with live progress, backup first, and desktop confirm modals.

Smart Summaries, Suggestions & Deposits Throughout Your .MDs

MD.Brain maintains an organized Summary & Suggestions section while also making intelligent Smart .MD Deposits directly into your approved .MDs — at the top, bottom, or where the information belongs, based on your settings.

Smart Summaries & Suggestions

  • Maintains an organized intelligence section for each approved .MD
  • Re-reads the entire file during Full File Update
  • Uses the .MD, Guidance, Strategies, and valuable Cursor knowledge

Smart .MD Deposits

  • Adds valuable new knowledge directly into the correct approved .MD
  • Can deposit at the top, bottom, or intelligently where the information belongs
  • Placement follows your deposit settings — Deep Mind picks the right file and location

Explore the full Cleanup tab

.MD Brain's Auto-Clean Tool — the full path

One continuous operator console from status tiles through Step 3 — Sync and Audit run first so Cloud Brain captures signal before anything destructive.

MD.Brain Cleanup tab — status tiles, Manual Clean Functions, and Auto-Clean Steps 1 through 3
Status tiles

Know how bogged down Cursor is before touching anything.

More

Live Bog Down score, Cursor disk footprint, chat file count, cache size, and audit keep/discard counts — so you know whether cleanup is worth running before you touch anything.

Manual Clean

Use targeted cleanup when you already know exactly what you want.

More

Apply presets like After audit (recommended) or Maximum squeeze, refresh stats, clear cache, and mix individual actions with preview + confirm.

Auto-Clean

Then walk the guided path from top to bottom.

More

Guided Sync, Audit, then run only what you check in Step 3. Protect Cursor Chats lives on the Windows Command Panel (desktop-only picker). Cleanup and Playbook are desktop-only — Web Admin is Monitor, Your Guidance, History, and Settings.

Step 1
Sync First

Preserve the valuable knowledge first.

More

Step 1 Sync uploads your .MDs to the cloud before cleanup continues. Smart .MD Deposits and managed Summary & Suggestions sections update for approved .MDs when those features are on.

Step 2
Audit Chats

Mark what is safe to clear — automatically.

More

Run Full Audit using your Delete and Overlap thresholds — no manual chat-by-chat review required.

Step 2.5
Protect Chats

Save the threads you still need before anything destructive runs.

More

Search every chat, open any one in .MD Brain Chat Viewer, then toggle ON what must survive Step 3.

Step 3
Clean

Run only what you checked — with preview and confirm.

More

Delete flagged chats, clear cache, shrink Composer DB, and more. Backup first, live progress, desktop confirm modals.

Every destructive step previews first and asks for desktop confirm — customer .md files are never deleted.

Organized .MDs

Go-Back Protected Full File Update and Auto-deposits each receive a versioned Go-Back point before MD.Brain writes to your approved .MDs. Restore via Web Admin → History & .MD Viewer → .MD Version Go-Back.

Both capabilities draw on your .MDs, Guidance, Strategies, and valuable Cursor knowledge. Full File Update can curate deposits and refresh the Summary — length scales to the .MD (short files stay ~500 words; large specs may use 2,000+). Your original content outside managed sections is never changed. After install, set Approved Scope, then enable Auto-Sync, Smart .MD Deposits, and Smart .MD Summaries in Your Guidance.

.MD Brain learns from your .MD files on the left, and from Strategies, valuable Cursor knowledge, and project decisions on the right. Guidance and Strategies also sit above the Brain. A simple loop connects your Cursor work, preservation, Smart .MD Deposits, Summary and Suggestions, and better context for the next session.

What .MD Brain learns from
Your .MD Files
Guidance & Strategies

Cleaner / Faster Cursor • Useful Suggestions Smart .MD Deposits • Organized .MDs

Strategies
Valuable Cursor Knowledge
Project Decisions

A Simple Intelligence Loop

Cursor work

Chats • code • decisions

Sync & audit

Capture signal • KEEP / DISCARD

Smart deposits + summaries

Codex + Guidance → correct .MD placement

Cloud Brain persists

Excerpts • rationale • Go-Back

Safe cleanup & new work

Lean Cursor → smarter next session

Cursor is where work happens. MD.Brain Cloud makes the valuable knowledge durable — then cleanup removes local weight without organizational amnesia. See the complete flywheel.

Cloud Brain

Your Intelligence Survives the Cursor Session

What MD.Brain Cloud adds beyond the local Cursor session. Cursor is where valuable work happens. MD.Brain Cloud makes sure the valuable knowledge, reasoning, history, and codex state can continue to exist and remain useful — even after local Cursor data is cleaned.

MD.Brain Cloud gives your company’s intelligence continuity. Cursor sessions can end. Chats can be cleaned. Developers can switch machines. A Full File Update can refresh summaries or curate deposits. Your codex history, deposit rationale, and valuable chat signal can remain available through MD.Brain.

Recovery

.MD Go-Back

Version history for your living codex.

Before managed AI changes — Full File Update and Auto-deposits — MD.Brain creates a versioned snapshot of the approved .md. Preview the previous version, compare what changed, and restore from Web Admin → History & .MD Viewer → .MD Version Go-Back. Manual edits outside AI-managed sections are not versioned.

  • Preview previous versions
  • Compare what changed
  • Restore per file from Web Admin

Per-file recovery in Web Admin — separate from desktop Cleanup → Go-Back Tools (chat database and Cloud Brain database backups). MD.Brain can improve the Brain without forcing you to trust every AI change permanently.

History

Chat Excerpts + Audit History

The valuable signal survives local cleanup.

When Cursor work is synchronized, MD.Brain Cloud preserves useful conversation signal — curated excerpts and bounded metadata, not a blind upload of the entire local Cursor database:

  • Chat metadata & curated excerpts
  • KEEP / DISCARD audit decisions
  • Value scoring, timestamps & associated .md

Inspect what mattered through History & .MD Viewer even if the original local Cursor conversation was removed during cleanup.

Delete local weight without creating organizational amnesia.

Your local chat can disappear without taking all of its useful history with it.

Codex intelligence

Smart .MD Deposits + Rationale

Keep the knowledge, not just the database row.

The most valuable outcome is not storing old chat records forever. MD.Brain converts useful Cursor knowledge into durable codex intelligence, making Smart Deposits into the appropriate approved .md at the top, bottom, or contextually appropriate location according to your settings. Smart Summaries & Suggestions still maintain their dedicated managed section. Inspect the history and rationale behind every deposit.

MD.Brain doesn’t preserve valuable work merely as cloud database records — it deposits useful knowledge back into the living .MD codex.

Raw conversation history is temporary. Useful company knowledge should not be.

Cursor conversation

Where work happens

Audit

KEEP / DISCARD

Deep Mind

Codex + Guidance

Useful knowledge

Synthesized signal

Correct .md

Top • Bottom • Where Needed

Persistent intelligence

Living company Brain

Preserve intelligence first. Clean second.

MD.Brain’s cloud layer enables this sequence — cleanup comes last, after the important signal is already safe.

  1. 1
    Sync

    Capture the valuable signal.

  2. 2
    Audit

    Determine what deserves to survive.

  3. 3
    Deep Mind

    Understand the work using the codex + Guidance.

  4. 4
    Smart Deposits + Summaries

    Preserve knowledge in the appropriate .md — placed where it belongs.

  5. 5
    Cloud History

    Retain excerpts, decisions, rationale, and Go-Back recovery points.

  6. 6
    Clean Cursor

    Remove unnecessary local weight with dramatically more confidence.

MD.Brain is not “delete Cursor chats to make Cursor faster.”

MD.Brain is “build a persistent company Brain first, then safely remove the local clutter that no longer needs to carry your company’s memory.”

The complete MD.Brain flywheel

Cursor work Sync valuable signal Audit — KEEP / DISCARD Deep Mind Smart .MD Deposits + Summaries Cloud Brain Safe Cursor cleanup New work

That is why cleanup is safe. That is why the Deep Mind can keep learning. And that is why your .md codex becomes a living company Brain instead of a folder full of markdown files.

See MD.Brain on your desktop and in the cloud

The Windows widget is for daily work on your PC. Cloud Admin is your Cloud Brain control center — persistent intelligence, Smart Deposits, summaries, History, and Go-Back — not just remote file viewing. One account — matched outcomes, not identical tab sets.

Windows desktop widget

Floats over Cursor while you work. Stay in Mini-Me for the chip row, or open the full Command Panel when you need every tab.

MD.Brain Mini-Me widget — compact sync and Cursor stats at a glance
Mini-Me Compact chip row — sync, phase, bog-down, and CPU at a glance.
MD.Brain desktop Command Panel — Monitor and Stats, Playbook, Cleanup, History, and Settings
Windows Desktop Command Panel Daily-use controls for Monitor & Stats, Playbook, Cleanup, History, and Settings.

Cloud Admin Command Center

Four browser tabs — Monitor, Your Guidance, History & .MD Viewer, and Settings. Cleanup and Playbook live on the Windows Command Panel; AI Usage is inside Settings. Review Cloud Brain activity, deposits, Go-Back versions, and guidance from any machine.

MD.Brain Cloud Admin Command Center — Monitor, Your Guidance, History, and Settings
Cloud Admin Command Center Monitor, Your Guidance, History, and Settings. Review Cloud Brain activity, .MD Brain Deposits, your codex, Go-Back versions, guidance, and system settings from the browser.
MD.Brain Admin History — .MD Brain Deposits records
.MD Brain Deposits Durable codex intelligence — not just cloud database rows. Smart Deposits land in the correct approved .MD at the top, bottom, or where needed, with inspectable rationale.