apply-phd-email

---
name: workspace-filesystem
description: The virtual filesystem layout of this workspace.
---

# Virtual Filesystem

You work in a terminal over a virtual filesystem. Read files with shell
commands; service operations are listed in SKILL.md.

| Path | Description |
|---|---|
| `/workspace` | Agent workspace; current directory and home (`~`). |
| `/tmp` | Temporary files. |
| `/dev` | Device files: `null` and `zero` (mounted automatically). |
| `/mail` | Mailbox, read-only. Directories are IMAP folders; change them with the `emails` CLI. |

## `/mail` layout

```
/mail/<folder>/<yyyy-mm-dd>/<subject>__<uid>.email.json
/mail/<folder>/<yyyy-mm-dd>/<subject>__<uid>/<attachment>
```

Folders include `INBOX`, `Sent`, `Drafts`. Read message JSON and attachments
with shell commands. Subjects are sanitized; list directories to find paths.

/mail/<folder>/<yyyy-mm-dd>/<subject>__<uid>.email.json
/mail/<folder>/<yyyy-mm-dd>/<subject>__<uid>/<attachment>

---
name: workspace-commands
description: The shell commands, task tools, and python3 interpreter available in this workspace.
---

# Available commands

Standard Unix commands, among them:

    cat  head  tail  ls  find  grep  wc  sort  uniq  cut  tr  sed  awk
    diff  tee  xargs  jq  unzip  curl

with pipes, `>` redirection, `$(...)` substitution and `$'...'`.

The task CLIs below are registered with this shell rather than installed
as files; do not inspect them with `which`, `file` or `/usr/bin`.

## pdf-tools

Use `pdf-tools <command> '<JSON arguments>'`. Run
`pdf-tools <command> --help` to get more information.

| Command | Arguments | Description |
|---|---|---|
| `pdf-tools read-pdf-pages` | `{pdf_file_path: str, start_page?: int = 1, end_page?: int = 1}` | Read content from PDF file for specified page range. Supports both local file paths and URLs. For URLs, the PDF will be downloaded to a temporary directory and cached for future use. Note: Avoid reading too many pages at once (recommended: <50 pages) to prevent errors. Args: pdf_file_path: Path to the PDF file or URL to PDF start_page: Starting page number (default: 1) end_page: Ending page number (default: 1) Returns: Extracted text content from the specified pages |
| `pdf-tools get-pdf-info` | `{pdf_file_path: str}` | Get basic information about a PDF file including page count. Supports both local file paths and URLs. For URLs, the PDF will be downloaded to a temporary directory and cached for future use. Args: pdf_file_path: Path to the PDF file or URL to PDF Returns: Basic information about the PDF file |
| `pdf-tools merge-pdfs` | `{pdf_paths: list[str], output_path: str}` | Merge multiple PDF files into one. Supports both local file paths and URLs. URLs will be downloaded to temporary files before merging. Mixed local and URL paths are supported. Args: pdf_paths: List of paths to PDF files to merge (in order) - can include URLs output_path: Path where the merged PDF will be saved (must be local path) Returns: Success message with merge details or error message |
| `pdf-tools extract-pdf-pages` | `{source_path: str, page_numbers: list[int], output_path: str}` | Extract specific pages from a PDF and create a new PDF. Supports URLs for source PDF. The source PDF will be downloaded to a temporary directory if it's a URL. Output path must be a local file path. Args: source_path: Path to the source PDF file or URL to PDF page_numbers: List of page numbers to extract (1-indexed) output_path: Path where the new PDF will be saved (must be local path) Returns: Success message with extraction details or error message |
| `pdf-tools search-pdf-content` | `{pdf_file_path: str, pattern: str, page_size?: int = 10}` | Search for regex pattern in PDF content and return paginated results. Supports both local file paths and URLs. For URLs, the PDF will be downloaded to a temporary directory and cached for future use. Args: pdf_file_path: Path to the PDF file or URL to PDF pattern: Regular expression pattern to search for page_size: Number of results per page (10-50, default: 10) Returns: Search results with UUID for pagination, or error message |
| `pdf-tools search-pdf-next-page` | `{search_id: str}` | Get next page of search results. Args: search_id: Search session ID from previous search Returns: Next page of search results or error message |
| `pdf-tools search-pdf-prev-page` | `{search_id: str}` | Get previous page of search results. Args: search_id: Search session ID from previous search Returns: Previous page of search results or error message |
| `pdf-tools search-pdf-go-page` | `{search_id: str, page_number: int}` | Go to specific page of search results. Args: search_id: Search session ID from previous search page_number: Page number to go to (1-indexed) Returns: Specified page of search results or error message |
| `pdf-tools search-pdf-info` | `{search_id: str}` | Get information about a search session. Args: search_id: Search session ID from previous search Returns: Information about the search session |

## emails

Use `emails <command> '<JSON arguments>'`. Run `emails <command> --help` to
get more information.

| Command | Arguments | Description |
|---|---|---|
| `emails get-emails` | `{folder?: str = "INBOX", page?: int = 1, page_size?: int = 20}` | Get paginated list of emails from specified folder Args: folder: Email folder name (default: INBOX) page: Page number starting from 1 (default: 1) page_size: Number of emails per page (default: 20) |
| `emails read-email` | `{email_id: str}` | Read full content of a specific email Args: email_id: Email ID to read |
| `emails search-emails` | `{query: str, folder?: str = "INBOX", page?: int = 1, page_size?: int = 20}` | Search emails with query string (sorted by date descending) Args: query: Search query (subject, from, body content) folder: Folder to search in (default: INBOX) page: Page number starting from 1 (default: 1) page_size: Number of results per page (default: 20) |
| `emails send-email` | `{to: str, subject: str, body: str, html_body?: str = null, cc?: str = null, bcc?: str = null, attachments?: list[str] = null}` | Send an email with optional HTML body, CC, BCC, and attachments Args: to: Recipient email address(es), comma-separated subject: Email subject body: Plain text body html_body: HTML body content (optional) cc: CC recipients, comma-separated (optional) bcc: BCC recipients, comma-separated (optional) attachments: List of file paths to attach (optional) |
| `emails reply-email` | `{email_id: str, body: str, html_body?: str = null, cc?: str = null, bcc?: str = null, reply_all?: bool = false}` | Reply to an email Args: email_id: ID of email to reply to body: Reply message body (plain text) html_body: Reply message body (HTML, optional) cc: Additional CC recipients (optional) bcc: BCC recipients (optional) reply_all: Whether to reply to all recipients (default: False) |
| `emails forward-email` | `{email_id: str, to: str, body?: str = null, html_body?: str = null, cc?: str = null, bcc?: str = null}` | Forward an email to other recipients Args: email_id: ID of email to forward to: Recipients to forward to body: Additional message body (optional) html_body: Additional HTML message body (optional) cc: CC recipients (optional) bcc: BCC recipients (optional) |
| `emails delete-email` | `{email_id: str}` | Delete an email Args: email_id: Email ID to delete |
| `emails move-email` | `{email_id: str, target_folder: str}` | Move email to another folder Args: email_id: Email ID to move target_folder: Target folder name |
| `emails mark-emails` | `{email_ids: list[str], status: str}` | Mark multiple emails with status (read/unread/important/not_important) Args: email_ids: List of email IDs to mark status: Status to set (read, unread, important, not_important) |
| `emails move-emails` | `{email_ids: list[str], target_folder: str}` | Move multiple emails to another folder with improved ID synchronization Args: email_ids: List of email IDs to move target_folder: Target folder name |
| `emails delete-emails` | `{email_ids: list[str]}` | Delete multiple emails with improved ID synchronization Args: email_ids: List of email IDs to delete |
| `emails get-folders` | `{}` | Get list of available email folders |
| `emails create-folder` | `{folder_name: str}` | Create new email folder Args: folder_name: Name of folder to create |
| `emails delete-folder` | `{folder_name: str}` | Delete email folder Args: folder_name: Name of folder to delete |
| `emails get-mailbox-stats` | `{folder_name?: str = null}` | Get mailbox statistics Args: folder_name: Specific folder name (optional, defaults to all folders) |
| `emails get-unread-count` | `{folder_name?: str = null}` | Get unread message count Args: folder_name: Specific folder name (optional, defaults to all folders) |
| `emails check-connection` | `{}` | Check email server connection status |
| `emails get-email-headers` | `{email_id: str}` | Get complete email headers for technical analysis Args: email_id: Email ID to get headers for |
| `emails save-draft` | `{subject: str, body: str, html_body?: str = null, to?: str = null, cc?: str = null, bcc?: str = null}` | Save email draft Args: subject: Email subject body: Plain text body html_body: HTML body content (optional) to: Recipient email address(es) (optional) cc: CC recipients (optional) bcc: BCC recipients (optional) |
| `emails get-drafts` | `{page?: int = 1, page_size?: int = 20}` | Get list of saved drafts Args: page: Page number starting from 1 (default: 1) page_size: Number of drafts per page (default: 20) |
| `emails update-draft` | `{draft_id: str, subject?: str = null, body?: str = null, html_body?: str = null, to?: str = null, cc?: str = null, bcc?: str = null}` | Update existing draft Args: draft_id: Draft ID to update subject: Email subject (optional) body: Plain text body (optional) html_body: HTML body content (optional) to: Recipient email address(es) (optional) cc: CC recipients (optional) bcc: BCC recipients (optional) |
| `emails delete-draft` | `{draft_id: str}` | Delete draft Args: draft_id: Draft ID to delete |
| `emails export-emails` | `{folder?: str = null, export_path?: str = "emails_export.json", max_emails?: int = null, export_all_folders?: bool = false}` | Export emails to file for backup Args: folder: Specific folder to export (mutually exclusive with export_all_folders) export_path: Path where to save the export file max_emails: Maximum number of emails to export (optional, exports all if not specified) export_all_folders: Export from all folders instead of just one (default: False) |
| `emails import-emails` | `{import_path: str, target_folder?: str = null, preserve_folders?: bool = true}` | Import emails from backup file to IMAP server Args: import_path: Path to import file (.json or .eml) or a directory target_folder: Target folder for imported emails (if preserve_folders=False) preserve_folders: Whether to preserve original folder structure (default: True) |
| `emails download-attachment` | `{email_id: str, attachment_filename: str}` | Download email attachment to configured download path Args: email_id: Email ID containing the attachment attachment_filename: Name of attachment to download |

## memory

Use `memory <command> '<JSON arguments>'`. Run `memory <command> --help` to
get more information.

| Command | Arguments | Description |
|---|---|---|
| `memory create-entities` | `{entities: list[{name: str, entityType: str, observations: list[str]}]}` | Create multiple new entities in the knowledge graph — `entities.name`: The name of the entity; `entities.entityType`: The type of the entity; `entities.observations`: An array of observation contents associated with the entity |
| `memory create-relations` | `{relations: list[{from: str, to: str, relationType: str}]}` | Create multiple new relations between entities in the knowledge graph. Relations should be in active voice — `relations.from`: The name of the entity where the relation starts; `relations.to`: The name of the entity where the relation ends; `relations.relationType`: The type of the relation |
| `memory add-observations` | `{observations: list[{entityName: str, contents: list[str]}]}` | Add new observations to existing entities in the knowledge graph — `observations.entityName`: The name of the entity to add the observations to; `observations.contents`: An array of observation contents to add |
| `memory delete-entities` | `{entityNames: list[str]}` | Delete multiple entities and their associated relations from the knowledge graph — `entityNames`: An array of entity names to delete |
| `memory delete-observations` | `{deletions: list[{entityName: str, observations: list[str]}]}` | Delete specific observations from entities in the knowledge graph — `deletions.entityName`: The name of the entity containing the observations; `deletions.observations`: An array of observations to delete |
| `memory delete-relations` | `{relations: list[{from: str, to: str, relationType: str}]}` | Delete multiple relations from the knowledge graph — `relations`: An array of relations to delete; `relations.from`: The name of the entity where the relation starts; `relations.to`: The name of the entity where the relation ends; `relations.relationType`: The type of the relation |
| `memory read-graph` | `{}` | Read the entire knowledge graph |
| `memory search-nodes` | `{query: str}` | Search for nodes in the knowledge graph based on a query — `query`: The search query to match against entity names, types, and observation content |
| `memory open-nodes` | `{names: list[str]}` | Open specific nodes in the knowledge graph by their names — `names`: An array of entity names to retrieve |

## git

Use `git --help` for Git operations on workspace repositories.

## python3

Execute Python code directly under the agent workspace and return stdout
and stderr. Code can be pasted into a `.py` file and run with `python3`.

Python cannot launch subprocesses or make direct network requests. Run the
documented service commands directly in the shell. Use Python for local
file processing and generating JSON arguments.

cat  head  tail  ls  find  grep  wc  sort  uniq  cut  tr  sed  awk
diff  tee  xargs  jq  unzip  curl