@ncukondo/reference-manager 0.14.0 → 0.15.0

package/README.md

@@ -43,7 +43,7 @@ Streamline your writing workflow:
 
 ```bash
 # Find and select references interactively
-ref search -i "machine learning"
+ref search -t "machine learning"
 # → Select references with Space, then export as BibTeX or generate citations
 
 # Generate citations
@@ -221,20 +221,38 @@ ref completion uninstall
 After installation, restart your shell or source the config file. Then:
 
 ```bash
-ref <TAB>                    # Shows: list search add remove ...
+ref <TAB>                    # Shows: list search add remove attach ...
 ref list --<TAB>             # Shows: --json --sort --limit ...
 ref list --sort <TAB>        # Shows: created updated published ...
 ref cite <TAB>               # Shows: smith2023 jones2024 ...
 ref cite smith<TAB>          # Shows: smith2023 smith2024-review
+ref attach <TAB>             # Shows: open add list get detach sync
+ref attach add <ID> --role <TAB>  # Shows: fulltext supplement notes draft
 ```
 
 Completion includes:
 - Subcommands and options
-- Option values (sort fields, citation styles, etc.)
+- Option values (sort fields, citation styles, attachment roles, etc.)
 - Dynamic reference IDs from your library
 
 ## CLI Reference
 
+### Interactive ID Selection
+
+When you invoke certain commands without specifying IDs in a TTY environment, an interactive search prompt appears:
+
+```bash
+# These commands support interactive selection when ID is omitted
+ref cite                  # Select references → generate citation
+ref edit                  # Select references → open in editor
+ref remove                # Select reference → confirm deletion
+ref update                # Select reference → update flow
+ref fulltext attach       # Select reference → attach file
+ref fulltext open         # Select reference → open file
+```
+
+This makes it easy to quickly find and act on references without remembering citation keys.
+
 ### Basic Commands
 
 ```bash
@@ -255,16 +273,16 @@ ref search "author:jones year:2024"
 ref search "title:\"deep learning\""
 
 # Interactive search (with real-time filtering)
-ref search -i                         # Start interactive mode
-ref search -i "machine learning"      # Pre-fill query
+ref search -t                         # Start interactive mode
+ref search -t "machine learning"      # Pre-fill query
 
 # Export raw CSL-JSON (for pandoc, jq, etc.)
 ref export smith2024                          # Single reference (as object)
 ref export smith2024 jones2023                # Multiple references (as array)
 ref export --all                              # All references
 ref export --search "author:smith"            # Search results
-ref export smith2024 --format yaml            # YAML format
-ref export --all --format bibtex              # BibTeX format
+ref export smith2024 -o yaml                  # YAML format
+ref export --all -o bibtex                    # BibTeX format
 
 # Add references
 ref add paper.json                    # From CSL-JSON file
@@ -275,8 +293,8 @@ ref add pmid:25056061                 # From PubMed ID
 ref add "ISBN:978-4-00-000000-0"      # From ISBN
 cat references.json | ref add         # From stdin (file content)
 echo "10.1038/nature12373" | ref add  # From stdin (DOI auto-detect)
-echo "12345678" | ref add --format pmid  # From stdin (PMID)
-echo "ISBN:978-4-00-000000-0" | ref add --format isbn  # From stdin (ISBN)
+echo "12345678" | ref add -i pmid     # From stdin (PMID)
+echo "ISBN:978-4-00-000000-0" | ref add -i isbn  # From stdin (ISBN)
 
 # Remove a reference
 ref remove smith2024
@@ -310,7 +328,16 @@ ref update smith2024 --set "abstract="
 # Generate citations
 ref cite smith2024
 ref cite smith2024 jones2023 --style apa
-ref cite smith2024 --style chicago-author-date --format html
+ref cite smith2024 --style chicago-author-date -o html
+
+# Interactive selection (no ID argument)
+ref cite
+# → Select references interactively → choose style → output citation
+
+# Additional options
+ref cite smith2024 --in-text                 # In-text citation: (Smith, 2024)
+ref cite smith2024 --csl-file ./custom.csl   # Use custom CSL file
+ref cite smith2024 --locale ja-JP            # Japanese locale
 ```
 
 ### Fulltext Management
@@ -341,6 +368,84 @@ ref fulltext detach smith2024 --pdf
 ref fulltext detach smith2024 --pdf --delete      # Also delete the file
 ```
 
+### Attachment Management
+
+A more flexible attachment system supporting multiple files per reference with role-based categorization:
+
+```bash
+# Open reference's attachment folder (for drag-and-drop file management)
+ref attach open smith2024                # Opens folder in file manager
+ref attach open smith2024 --print        # Print path only (for scripting)
+
+# Add attachments programmatically
+ref attach add smith2024 supplement.xlsx --role supplement
+ref attach add smith2024 notes.md --role notes
+ref attach add smith2024 draft-v1.docx --role draft --label v1
+ref attach add smith2024 file.pdf --move    # Move instead of copy
+ref attach add smith2024 file.pdf --force   # Overwrite existing
+
+# List attachments
+ref attach list smith2024                # List all attachments
+ref attach list smith2024 --role supplement  # Filter by role
+
+# Get attachment path
+ref attach get smith2024 supplement-data.xlsx
+
+# Sync metadata with filesystem (after manual file operations)
+ref attach sync smith2024                # Show pending changes (dry-run)
+ref attach sync smith2024 --yes          # Apply changes
+ref attach sync smith2024 --fix          # Also remove missing files from metadata
+
+# Detach files
+ref attach detach smith2024 supplement-data.xlsx
+ref attach detach smith2024 supplement-data.xlsx --delete  # Also delete file
+```
+
+**Available Roles:**
+- `fulltext` — Primary document (PDF or Markdown)
+- `supplement` — Supplementary materials, datasets
+- `notes` — Research notes
+- `draft` — Draft versions
+
+**Manual Workflow:**
+1. `ref attach open smith2024` — Opens folder in your file manager
+2. Drag and drop files into the folder
+3. `ref attach sync smith2024 --yes` — Updates metadata to include new files
+
+Files are organized by reference in directories named `Author-Year-ID-UUID` under the attachments directory.
+
+### Edit Command
+
+Edit references interactively using your preferred text editor:
+
+```bash
+# Edit single reference
+ref edit smith2024
+
+# Edit multiple references
+ref edit smith2024 jones2023
+
+# Edit by UUID
+ref edit --uuid 550e8400-e29b-41d4-a716-446655440000
+
+# Edit in JSON format (default is YAML)
+ref edit smith2024 --format json
+
+# Interactive selection (no ID argument)
+ref edit
+```
+
+**Editor selection** (same as Git):
+1. `$VISUAL` environment variable
+2. `$EDITOR` environment variable
+3. Platform fallback: `vi` (Linux/macOS) or `notepad` (Windows)
+
+**Features:**
+- Opens references in YAML or JSON format
+- Protected fields (uuid, timestamps, fulltext) shown as comments
+- Validation with re-edit option on errors
+- Date fields simplified to ISO format (`"2024-03-15"`)
+
 ### Output Formats
 
 | Format | Flag | Description |
@@ -401,8 +506,8 @@ Supported field prefixes: `id:`, `author:`, `title:`, `year:`, `doi:`, `pmid:`,
 Start an interactive search session with real-time filtering:
 
 ```bash
-ref search -i                    # Start with empty query
-ref search -i "machine learning" # Pre-fill the search query
+ref search -t                    # Start with empty query
+ref search -t "machine learning" # Pre-fill the search query
 ```
 
 **Features:**
@@ -491,7 +596,46 @@ auto_stop_minutes = 60
 | Variable | Description |
 |----------|-------------|
 | `REFERENCE_MANAGER_LIBRARY` | Override library file path |
-| `REFERENCE_MANAGER_FULLTEXT_DIR` | Override fulltext directory |
+| `REFERENCE_MANAGER_ATTACHMENTS_DIR` | Override attachments directory |
+
+### Config Command
+
+Manage configuration via CLI without manually editing TOML files:
+
+```bash
+# View all configuration
+ref config show
+ref config show -o json           # JSON format
+ref config show --sources         # Show where each value comes from
+
+# Get/set individual values
+ref config get citation.default_style
+ref config set citation.default_style chicago-author-date
+ref config set --local citation.default_style ieee  # Project-local config
+
+# Reset to default
+ref config unset citation.default_style
+
+# List all available keys
+ref config keys
+
+# Show config file locations
+ref config path
+
+# Open config in editor
+ref config edit
+ref config edit --local           # Edit project-local config
+```
+
+**Key categories:**
+- `library`, `log_level` — Core settings
+- `backup.*` — Backup configuration
+- `server.*` — HTTP server settings
+- `citation.*` — Citation defaults (style, locale, format)
+- `pubmed.*` — PubMed API credentials
+- `fulltext.*` — Fulltext storage
+- `cli.*` — CLI behavior (limits, sorting, TUI mode)
+- `mcp.*` — MCP server settings
 
 ## Data Format
 

package/dist/chunks/{action-menu-DNlpGiwS.js → action-menu-DvwR6nMj.js}

@@ -1,5 +1,5 @@
-import { f as formatBibtex } from "./index-UpzsmbyY.js";
-import { f as formatBibliographyCSL } from "./index-4KSTJ3rp.js";
+import { f as formatBibtex } from "./index-Bv5IgsL-.js";
+import { f as formatBibliographyCSL } from "./index-DHgeuWGP.js";
 const ACTION_CHOICES = [
   { name: "output-ids", message: "Output IDs (citation keys)", value: "output-ids" },
   { name: "output-csl-json", message: "Output as CSL-JSON", value: "output-csl-json" },
@@ -116,4 +116,4 @@ export {
   runActionMenu,
   runStyleSelectPrompt
 };
-//# sourceMappingURL=action-menu-DNlpGiwS.js.map
+//# sourceMappingURL=action-menu-DvwR6nMj.js.map

package/dist/chunks/{action-menu-DNlpGiwS.js.map → action-menu-DvwR6nMj.js.map}

@@ -1 +1 @@
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+{"version":3,"file":"action-menu-DvwR6nMj.js","sources":["../../src/features/interactive/action-menu.ts"],"sourcesContent":["/**\n * Action menu for interactive search mode.\n * Allows users to perform actions on selected references.\n */\n\nimport type { CslItem } from \"../../core/csl-json/types.js\";\nimport { formatBibliographyCSL, formatBibtex } from \"../format/index.js\";\n\n/**\n * Action types available in the action menu.\n */\nexport type ActionType =\n  | \"output-ids\"\n  | \"output-csl-json\"\n  | \"output-bibtex\"\n  | \"cite-apa\"\n  | \"cite-choose\"\n  | \"cancel\";\n\n/**\n * Result from action menu selection.\n */\nexport interface ActionMenuResult {\n  /** Selected action type */\n  action: ActionType;\n  /** Generated output (empty for cancel) */\n  output: string;\n  /** Whether the prompt was cancelled */\n  cancelled: boolean;\n}\n\n/**\n * Result from style selection prompt.\n */\nexport interface StyleSelectResult {\n  /** Selected style (undefined if cancelled) */\n  style?: string;\n  /** Whether the prompt was cancelled */\n  cancelled: boolean;\n}\n\n/**\n * Choice definition for Enquirer Select prompt.\n */\ninterface SelectChoice {\n  name: string;\n  message: string;\n  value: ActionType | string;\n}\n\n/**\n * Available action choices for the action menu.\n */\nexport const ACTION_CHOICES: SelectChoice[] = [\n  { name: \"output-ids\", message: \"Output IDs (citation keys)\", value: \"output-ids\" },\n  { name: \"output-csl-json\", message: \"Output as CSL-JSON\", value: \"output-csl-json\" },\n  { name: \"output-bibtex\", message: \"Output as BibTeX\", value: \"output-bibtex\" },\n  { name: \"cite-apa\", message: \"Generate citation (APA)\", value: \"cite-apa\" },\n  { name: \"cite-choose\", message: \"Generate citation (choose style)\", value: \"cite-choose\" },\n  { name: \"cancel\", message: \"Cancel\", value: \"cancel\" },\n];\n\n/**\n * Available style choices for citation style selection.\n * Uses BUILTIN_STYLES from config/csl-styles.ts\n */\nexport const STYLE_CHOICES: SelectChoice[] = [\n  { name: \"apa\", message: \"APA\", value: \"apa\" },\n  { name: \"vancouver\", message: \"Vancouver\", value: \"vancouver\" },\n  { name: \"harvard\", message: \"Harvard\", value: \"harvard\" },\n];\n\n/**\n * Run the style selection prompt.\n */\n\n/**\n * Generate output for the given action and items.\n */\nfunction generateOutput(action: ActionType, items: CslItem[], style = \"apa\"): string {\n  switch (action) {\n    case \"output-ids\":\n      return items.map((item) => item.id).join(\"\\n\");\n\n    case \"output-csl-json\":\n      return JSON.stringify(items, null, 2);\n\n    case \"output-bibtex\":\n      return formatBibtex(items);\n\n    case \"cite-apa\":\n      return formatBibliographyCSL(items, { style: \"apa\" });\n\n    case \"cite-choose\":\n      return formatBibliographyCSL(items, { style });\n\n    case \"cancel\":\n      return \"\";\n\n    default:\n      return \"\";\n  }\n}\n\n/**\n * Process the selected action and generate result.\n */\nasync function processAction(action: ActionType, items: CslItem[]): Promise<ActionMenuResult> {\n  // Handle cite-choose: prompt for style first\n  if (action === \"cite-choose\") {\n    const styleResult = await runStyleSelectPrompt();\n    if (styleResult.cancelled) {\n      return {\n        action: \"cancel\",\n        output: \"\",\n        cancelled: true,\n      };\n    }\n    return {\n      action,\n      output: generateOutput(action, items, styleResult.style),\n      cancelled: false,\n    };\n  }\n\n  // Handle cancel\n  if (action === \"cancel\") {\n    return {\n      action,\n      output: \"\",\n      cancelled: true,\n    };\n  }\n\n  // Handle other actions\n  return {\n    action,\n    output: generateOutput(action, items),\n    cancelled: false,\n  };\n}\n\nexport async function runStyleSelectPrompt(): Promise<StyleSelectResult> {\n  // Dynamic import to allow mocking in tests\n  // enquirer is a CommonJS module, so we must use default import\n  const enquirer = await import(\"enquirer\");\n  const Select = (enquirer.default as unknown as Record<string, unknown>).Select as new (\n    options: Record<string, unknown>\n  ) => { run(): Promise<string> };\n\n  const promptOptions = {\n    name: \"style\",\n    message: \"Select citation style:\",\n    choices: STYLE_CHOICES,\n  };\n\n  try {\n    const prompt = new Select(promptOptions);\n    const result = (await prompt.run()) as string;\n\n    return {\n      style: result,\n      cancelled: false,\n    };\n  } catch (error) {\n    // Enquirer throws an empty string when cancelled\n    if (error === \"\" || (error instanceof Error && error.message === \"\")) {\n      return {\n        cancelled: true,\n      };\n    }\n    throw error;\n  }\n}\n\n/**\n * Run the action menu for selected references.\n *\n * @param items - 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package/dist/chunks/{file-watcher-D2Y-SlcE.js → file-watcher-B_WpVHSV.js}

@@ -1684,30 +1684,30 @@ export {
   FileWatcher as F,
   Library as L,
   Reference as R,
-  computeHash as a,
-  sortResults as b,
+  sortOrderSchema as a,
+  sortFieldSchema as b,
   computeFileHash as c,
-  detectDuplicate as d,
-  CslItemSchema as e,
-  parseCslJson as f,
-  serializeCslJson as g,
-  generateId as h,
-  generateIdWithCollisionCheck as i,
-  normalizeText as j,
-  generateUuid as k,
-  isValidUuid as l,
-  ensureCustomMetadata as m,
+  computeHash as d,
+  sortResults as e,
+  detectDuplicate as f,
+  CslItemSchema as g,
+  parseCslJson as h,
+  serializeCslJson as i,
+  generateId as j,
+  generateIdWithCollisionCheck as k,
+  normalizeText as l,
+  generateUuid as m,
   normalize as n,
-  extractUuidFromCustom as o,
+  isValidUuid as o,
   pickDefined as p,
-  sortOrderSchema as q,
-  paginationOptionsSchema as r,
+  ensureCustomMetadata as q,
+  extractUuidFromCustom as r,
   search as s,
   tokenize as t,
-  sortFieldSchema as u,
-  searchSortFieldSchema as v,
+  searchSortFieldSchema as u,
+  paginationOptionsSchema as v,
   writeCslJson as w,
   tokenizer as x,
   matcher as y
 };
-//# sourceMappingURL=file-watcher-D2Y-SlcE.js.map
+//# sourceMappingURL=file-watcher-B_WpVHSV.js.map