What Is a Project, and Where Do My Files Go?
Illustrated guide + structure diagram | For academic users with no technical background | Understand how the project folder maps to the sidebar
The first time you use Scholardo, it asks you to "create a project and pick a folder." A lot of people's first reaction is: what exactly is a project? Where do my PDFs, notes, and drafts go? This guide clears that up.
The Welcome screen already sums it up in one line (A7): "A project is a folder for one paper or topic. Your sources, notes, and AI chats all live inside it."
In One Sentence: A Project Is a Home for One Paper
A Scholardo project is just an ordinary folder on your disk. Your literature PDFs, notes, drafts, and AI conversation records all live inside this one folder. Want to back it up? Copy the whole folder. Moving to another computer? Move the whole folder. It isn't hidden away in some database — it's a folder you can see right there in Finder.
The 4 Sidebar Tabs ↔ Folders
Scholardo has 4 main tabs on the left, and each tab maps to a real subfolder inside your project folder:
| Sidebar tab | Folder | What goes in it |
|---|---|---|
| Sources | sources/ | Your input materials: literature PDFs, references, feeds |
| Notebook | notebook/ | Your notes and to-dos |
| Outputs | outputs/ | Your output: drafts, exports |
| Agent | agent/ | The AI's memory, rules, skills, and other config |
📌 These 4 tab names currently display in English (Sources / Notebook / Outputs / Agent), even when the system language is set to Chinese.
Sources Splits into Three More
Open Sources, and the content area has three more sub-categories:
- Docs →
sources/docs/: your literature PDFs go here (drag them in, or use "Save to Sources/Docs"). - Refs →
sources/refs/: references / BibTeX entries. - Feeds →
sources/feeds/: RSS feed sources.
💡 So when earlier guides said "put the PDF in sources," more precisely it goes into Sources › Docs (
sources/docs/). When you drag a PDF into the Sources view, Scholardo automatically files it under Docs.
What the Folder Structure Looks Like (in Finder)
Open your project folder in Finder and it looks roughly like this (simplified):
My Paper/
├── project.yml ← project config
├── sources/ ← [Sources tab] input materials
│ ├── docs/ ← literature PDFs go here
│ ├── refs/ ← references / BibTeX
│ └── feeds/ ← RSS feeds
├── notebook/ ← [Notebook tab]
│ ├── notes/ ← notes
│ └── todo/ ← to-dos
├── outputs/ ← [Outputs tab] drafts / exports
├── agent/ ← [Agent tab] AI memory / rules / skills
└── .scholardo/ ← app-internal data (you can ignore it)
├── scholardo.db ← this project's index database
├── file-groups.json ← file grouping
└── reading-status.json ← reading progress
.scholardo/is a hidden folder that stores Scholardo's own index and state. You normally never need to touch it.
Privacy Boundary: the AI Can Only See This Project Folder
An important safety guarantee: in Scholardo, the AI can only read and write files inside your current project folder — it can't touch anything outside it. This isn't a matter of "reminding the AI to behave"; the app hard-blocks any out-of-bounds access at a low level — if the AI tries to read or write a path outside the project root, it's rejected outright (with an error like Path is outside the project root).
In other words: only what you put into this project is what the AI can see; things on your Desktop or in other folders are out of its reach. To have the AI reference some material, put it into the matching tab / folder.
Shot list (screenshot checklist)
Capture the Scholardo UI from the current release. Use a simplified structure in diagrams, and avoid showing real research materials.
| Asset | Content | UI source | Key callout |
|---|---|---|---|
| Fig 1 | Structure diagram: project folder → 4 subfolders ↔ 4 sidebar tabs, with mapping lines | Custom diagram | Label each line with the tab name (English) + its meaning |
| Fig 2 | Scholardo's 4 sidebar tabs (Sources / Notebook / Outputs / Agent) | Scholardo | Circle the 4 tab icons and names |
| Fig 3 | The Docs / Refs / Feeds sub-categories in the Sources content area, with a few PDFs under Docs | Scholardo | Circle "PDFs are filed under Docs" |
| Fig 4 | The project folder opened in Finder, matched against the structure tree above | Finder | Circle sources/docs, notebook, outputs |
| Fig 5 | Privacy-boundary diagram: inside the project folder = AI can see it; outside = out of reach | Custom diagram | "The AI can only see this project folder" |
Key callouts recap
- A project = an ordinary folder: visible in Finder, backed up / moved as a whole.
- 4 tabs ↔ 4 folders: Sources / Notebook / Outputs / Agent each map to a subfolder (names currently in English).
- PDFs go in Sources › Docs (
sources/docs/). - The AI can only see this project folder: out-of-bounds access is hard-blocked by the app.
Data Privacy Disclosure
When you ask the AI to read, summarize, or polish the manuscripts in your project, that content is sent to your chosen AI provider for processing. Two boundaries are worth stating: first, the AI can only access files inside the current project folder (out-of-bounds access is blocked by the app); second, once you actively start a conversation and have it read some material, that material's content is transmitted over the network to your chosen provider (Anthropic / OpenAI / DeepSeek, etc.) and handled under its privacy policy. If your research materials involve unpublished data, participant privacy, or confidentiality agreements, first confirm that sending them to a third-party AI service complies with your institution's requirements.