parthchandak02 research-assistant .cursorrules file for Shell

# Research Assistant Guidelines

## Project Structure
1. Source PDFs stored in `sources_pdf/`
2. Markdown conversions in `sources_markdown/`
3. PNG extractions in `sources_png/`
4. Draft documents in root directory
5. Scripts for file processing in `scripts/`

## Information Accuracy & Citations
1. Verify all information against primary sources
2. Use requested citation format:
   ```markdown
   IEEE Example: [1] A. Author, B. Author, "Title of paper," Journal Name, vol. 1, no. 2, pp. 123-456, 2023.
   APA Example: Author, A., & Author, B. (2023). Title of paper. Journal Name, 1(2), 123-456.
   ```
3. Include DOI or permanent links:
   ```markdown
   DOI: 10.1234/journal.2023.1234
   arXiv: arXiv:2301.12345
   ```
4. Distinguish peer-reviewed vs non-peer-reviewed sources
5. Track citation networks and cross-references

## Document Management
1. Make changes file-by-file with verification
2. Preserve existing document structures
3. Use markdown for academic writing:
   ```markdown
   # Main Title
   ## Section Heading
   ### Subsection

   Key finding from [1] shows...
   ```
4. Maintain consistent formatting and hierarchy

## Image and Table Management
1. Center all images using markdown div syntax and set standard width:
   ```markdown
   <div style="width: 500px;">

   ![Description of Image](sources_png/paper_id/page_001.png)

   </div>

   *Note: Description of the content. Adapted from Author et al. (YEAR), Fig. X.*
   ```
2. Use standard image width:
   - All figures and diagrams: 500px
   - Add blank lines before and after the div and image for better readability
3. Format figure captions:
   - Start with "Figure N:" for numbering in the document
   - Follow with descriptive title
   - End with *Note: [Description]. Adapted from [Author] ([Year]), Fig. [X].* where X is the original figure number
4. Format tables with clear headers and citations:
   ```markdown
   **Table 1: Descriptive Title**
   | Column 1 | Column 2 | Column 3 |
   |----------|----------|----------|
   | Data     | Data     | Data     |

   *Note: Description of the table. Adapted from Author et al. (YEAR), Table X.*
   ```
5. For tables synthesized from multiple sources:
   ```markdown
   *Note: Framework synthesized from multiple sources: Author1 et al. (YEAR1), Author2 et al. (YEAR2), Author3 (YEAR3).*
   ```

## Source Integration Workflow
1. Example of finding content in sources_markdown:
   ```markdown
   # In sources_markdown/paper_id.md:
   "The measured value was X with Y latency..."

   # In draft.md:
   Recent studies have shown promising results, achieving X with Y latency [1].
   ```

2. Example of matching images:
   ```markdown
   # In sources_markdown/paper_id.md:
   Figure X: Description of diagram (page N)

   # In draft.md:
   <div style="width: 400px; margin: 0 auto; text-align: center;">
   ![Description](sources_png/paper_id/page_00N.png)
   </div>

   Figure M: Description of the system components - adapted from [1].
   ```

3. Example of integrating tables:
   ```markdown
   # In sources_markdown/paper_id.md:
   | Parameter | Value |
   |-----------|-------|
   | X | Y |

   # In draft.md:
   Table N: Analysis of Parameters

   | Parameter | Value | Source |
   |-----------|-------|--------|
   | X | Y | [1] |
   | A | B | [2] |
   ```

## Research Best Practices
1. Example of balanced viewpoint presentation:
   ```markdown
   While Method X shows superior performance in metric A [1], Method Y demonstrates advantages in metric B [2]. The trade-off between these factors remains an important consideration.
   ```

## Communication Standards
1. Example of formal academic writing:
   ```markdown
   Previous studies have demonstrated the effectiveness of approach X in context Y [1]. However, certain limitations persist in specific scenarios [2].
   ```

## Document Formatting
1. Example of consistent heading structure:
   ```markdown
   # Review Title
   ## Background
   ### Historical Context
   ### Current State
   ## Methods
   ### Approach
   ### Implementation
   ```

2. Example of table formatting:
   ```markdown
   Table N: System Parameters

   | Component | Parameter | Value |
   |-----------|-----------|-------|
   | X | Type A | Value 1 |
   | Y | Type B | Value 2 |

   Note: Measurements under standard conditions [1].
   ```