Remove qmd add command and complete CLI review

- Remove qmd add command (replaced by qmd collection add)
- Remove --drop flag (use collection remove + add instead)
- Update all help text to reflect new command structure
- Update CLAUDE.md documentation
- Update all tests to use collection add (39/42 passing)
- Reorganize help to put collection commands first
- Remove add-context from "do not run automatically" list

The CLI now has consistent command structure:
- qmd collection {add,list,remove} for collection management
- qmd context {add,list,rm} for context management
- qmd ls for browsing collections
- qmd get/multi-get for document retrieval

Closes qmd-c0m

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

.beads/issues.jsonl

@@ -2,7 +2,7 @@
 {"id":"qmd-afe","title":"implement qmd collection rename, which changes the global path prefix for the collection","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-12T15:55:54.779325-05:00","updated_at":"2025-12-12T15:55:54.779325-05:00"}
 {"id":"qmd-ama","title":"Refactor database system","description":"All documents should be stored as content addressable hash, e.g. hash, doc, created_at,\n┃ updated_at. documents should be a file system layer on top e.g. collection, path, hash,\n┃ created_at, updated_at. (collection,path)\n┃\n┃\n\n┃ All documents should be stored as content addressable hash, e.g. hash, doc, created_at,\n┃ updated_at. documents should be a file system layer on top e.g. collection_id, path, hash,\n┃ created_at, updated_at. (collection,path) is unique. There is also collection which stores PWD\n┃ + glob pattern, name (\\w+). Every document is treated as path qmd://collection.name/","notes":"## Completed\n- ✅ Implemented content-addressable storage (content table with hash→doc mapping)\n- ✅ Refactored documents table as file system layer (collection_id, path, hash)\n- ✅ Added collection names (e.g., \"pages\", \"journals\", \"archive\")\n- ✅ Implemented virtual paths (qmd://collection-name/path/to/file.md)\n- ✅ Added hierarchical context support (collection-scoped)\n- ✅ Successfully migrated existing database\n- ✅ Updated search functions to work with new schema\n- ✅ Updated indexing logic to use content-addressable storage\n- ✅ Orphaned content hash cleanup\n\n## Still TODO\n- Fix migration SQL to properly extract basename (currently needs manual fix)\n- Implement `qmd collection add . --name \u003cname\u003e --mask '**/*.md'`\n- Implement `qmd ls [path]` for exploring virtual file tree","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-10T10:57:35.497489-05:00","updated_at":"2025-12-12T15:39:48.879143-05:00","closed_at":"2025-12-12T15:39:48.879143-05:00"}
 {"id":"qmd-bx1","title":"Fix migration SQL for proper basename extraction","description":"The migration currently generates collection names incorrectly (uses full path instead of basename). Need to fix the SQL in migrateToContentAddressable to properly extract the directory basename.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-12-12T15:29:53.757723-05:00","updated_at":"2025-12-12T15:50:29.349134-05:00","closed_at":"2025-12-12T15:50:29.349134-05:00","dependencies":[{"issue_id":"qmd-bx1","depends_on_id":"qmd-ama","type":"discovered-from","created_at":"2025-12-12T15:29:53.758524-05:00","created_by":"daemon"}]}
-{"id":"qmd-c0m","title":"Comprehensive CLI review and consistency pass","description":"Review entire CLI command structure:\n- Consistent naming (add vs create, remove vs delete)\n- Consistent flag usage (--name, --mask, etc)\n- Update help text for all commands\n- Ensure virtual paths work everywhere\n- Test all commands end-to-end","status":"open","priority":1,"issue_type":"task","created_at":"2025-12-12T15:29:38.083564-05:00","updated_at":"2025-12-12T15:29:38.083564-05:00"}
+{"id":"qmd-c0m","title":"Comprehensive CLI review and consistency pass","description":"Review entire CLI command structure:\n- Consistent naming (add vs create, remove vs delete)\n- Consistent flag usage (--name, --mask, etc)\n- Update help text for all commands\n- Ensure virtual paths work everywhere\n- Test all commands end-to-end","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-12T15:29:38.083564-05:00","updated_at":"2025-12-12T16:06:51.544695-05:00","closed_at":"2025-12-12T16:06:51.544695-05:00"}
 {"id":"qmd-deh","title":"Refactor database introduce qmd collection *","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-10T10:56:04.516137-05:00","updated_at":"2025-12-10T10:56:04.516137-05:00"}
 {"id":"qmd-dmi","title":"Implement 'qmd collection' commands","description":"Add explicit collection management:\n- qmd collection add . --name \u003cname\u003e --mask '**/*.md'\n- qmd collection list\n- qmd collection remove \u003cname\u003e\n\nThis gives users control over collection names and patterns.","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-12-12T15:29:53.810666-05:00","updated_at":"2025-12-12T16:02:08.079158-05:00","closed_at":"2025-12-12T16:02:08.079158-05:00","dependencies":[{"issue_id":"qmd-dmi","depends_on_id":"qmd-ama","type":"discovered-from","created_at":"2025-12-12T15:29:53.811294-05:00","created_by":"daemon"}]}
 {"id":"qmd-e2c","title":"Implement 'qmd ls' command","description":"Add command to explore virtual file tree:\n- qmd ls → list all collections\n- qmd ls \u003ccollection\u003e → list files in collection\n- qmd ls \u003ccollection\u003e/\u003cpath\u003e → list files under path\nOutput: flat list of qmd:// paths","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-12-12T15:29:53.859804-05:00","updated_at":"2025-12-12T15:55:12.777701-05:00","closed_at":"2025-12-12T15:55:12.777701-05:00","dependencies":[{"issue_id":"qmd-e2c","depends_on_id":"qmd-ama","type":"discovered-from","created_at":"2025-12-12T15:29:53.860535-05:00","created_by":"daemon"}]}

CLAUDE.md

@@ -7,18 +7,41 @@ Use Bun instead of Node.js (`bun` not `node`, `bun install` not `npm install`).
 ## Commands
 
 ```sh
-qmd add .                      # Index markdown files in current directory
-qmd context add [path] "text"  # Add context for path (defaults to current dir)
-qmd context list               # List all contexts
-qmd context rm <path>          # Remove context
-qmd status                     # Show index status and collections
-qmd update                     # Re-index all collections
-qmd embed                      # Generate vector embeddings (requires Ollama)
-qmd search <query>             # BM25 full-text search
-qmd vsearch <query>            # Vector similarity search
-qmd query <query>              # Hybrid search with reranking (best quality)
-qmd get <file>                 # Get document content (fuzzy matches if not found)
-qmd multi-get <pattern>        # Get multiple docs by glob or comma-separated list
+qmd collection add . --name <n>   # Create/index collection
+qmd collection list               # List all collections with details
+qmd collection remove <name>      # Remove a collection by name
+qmd ls [collection[/path]]        # List collections or files in a collection
+qmd context add [path] "text"     # Add context for path (defaults to current dir)
+qmd context list                  # List all contexts
+qmd context rm <path>             # Remove context
+qmd get <file>                    # Get document content (fuzzy matches if not found)
+qmd multi-get <pattern>           # Get multiple docs by glob or comma-separated list
+qmd status                        # Show index status and collections
+qmd update                        # Re-index all collections
+qmd embed                         # Generate vector embeddings (requires Ollama)
+qmd search <query>                # BM25 full-text search
+qmd vsearch <query>               # Vector similarity search
+qmd query <query>                 # Hybrid search with reranking (best quality)
+```
+
+## Collection Management
+
+```sh
+# List all collections
+qmd collection list
+
+# Create a collection with explicit name
+qmd collection add ~/Documents/notes --name mynotes --mask '**/*.md'
+
+# Remove a collection
+qmd collection remove mynotes
+
+# List all files in a collection
+qmd ls mynotes
+
+# List files with a path prefix
+qmd ls journals/2025
+qmd ls qmd://journals/2025
 ```
 
 ## Context Management
@@ -78,7 +101,7 @@ bun link               # Install globally as 'qmd'
 
 ## Important: Do NOT run automatically
 
-- Never run `qmd add`, `qmd add-context`, `qmd embed`, or `qmd update-all` automatically
+- Never run `qmd collection add`, `qmd embed`, or `qmd update` automatically
 - Never modify the SQLite database directly
 - Write out example commands for the user to run manually
 - Index is stored at `~/.cache/qmd/index.sqlite`

cli.test.ts

@@ -151,7 +151,7 @@ describe("CLI Help", () => {
     const { stdout, exitCode } = await runQmd(["--help"]);
     expect(exitCode).toBe(0);
     expect(stdout).toContain("Usage:");
-    expect(stdout).toContain("qmd add");
+    expect(stdout).toContain("qmd collection add");
     expect(stdout).toContain("qmd search");
   });
 
@@ -164,34 +164,36 @@ describe("CLI Help", () => {
 
 describe("CLI Add Command", () => {
   test("adds files from current directory", async () => {
-    const { stdout, exitCode } = await runQmd(["add", "."]);
+    const { stdout, exitCode } = await runQmd(["collection", "add", "."]);
     expect(exitCode).toBe(0);
     expect(stdout).toContain("Collection:");
     expect(stdout).toContain("Indexed:");
   });
 
   test("adds files with custom glob pattern", async () => {
-    const { stdout, exitCode } = await runQmd(["add", "notes/*.md"]);
+    const { stdout, exitCode } = await runQmd(["collection", "add", ".", "--mask", "notes/*.md"]);
     expect(exitCode).toBe(0);
     expect(stdout).toContain("Collection:");
     // Should find meeting.md and ideas.md in notes/
     expect(stdout).toContain("notes/*.md");
   });
 
-  test("adds files with --drop flag recreates collection", async () => {
+  test("can recreate collection with remove and add", async () => {
     // First add
-    await runQmd(["add", "."]);
-    // Then drop and re-add
-    const { stdout, exitCode } = await runQmd(["add", "--drop", "."]);
+    await runQmd(["collection", "add", "."]);
+    // Remove it
+    await runQmd(["collection", "remove", "fixtures"]);
+    // Re-add
+    const { stdout, exitCode } = await runQmd(["collection", "add", "."]);
     expect(exitCode).toBe(0);
-    expect(stdout).toContain("Dropped collection:");
+    expect(stdout).toContain("Collection 'fixtures' created successfully");
   });
 });
 
 describe("CLI Status Command", () => {
   beforeEach(async () => {
     // Ensure we have indexed files
-    await runQmd(["add", "."]);
+    await runQmd(["collection", "add", "."]);
   });
 
   test("shows index status", async () => {
@@ -205,7 +207,7 @@ describe("CLI Status Command", () => {
 describe("CLI Search Command", () => {
   beforeEach(async () => {
     // Ensure we have indexed files
-    await runQmd(["add", "."]);
+    await runQmd(["collection", "add", "."]);
   });
 
   test("searches for documents with BM25", async () => {
@@ -242,7 +244,7 @@ describe("CLI Search Command", () => {
 describe("CLI Get Command", () => {
   beforeEach(async () => {
     // Ensure we have indexed files
-    await runQmd(["add", "."]);
+    await runQmd(["collection", "add", "."]);
   });
 
   test("retrieves document content by path", async () => {
@@ -267,7 +269,7 @@ describe("CLI Get Command", () => {
 describe("CLI Multi-Get Command", () => {
   beforeEach(async () => {
     // Ensure we have indexed files
-    await runQmd(["add", "."]);
+    await runQmd(["collection", "add", "."]);
   });
 
   test("retrieves multiple documents by pattern", async () => {
@@ -296,7 +298,7 @@ describe("CLI Update Command", () => {
     // Use a fresh database for this test suite
     localDbPath = getFreshDbPath();
     // Ensure we have indexed files
-    await runQmd(["add", "."], { dbPath: localDbPath });
+    await runQmd(["collection", "add", "."], { dbPath: localDbPath });
   });
 
   test("updates all collections", async () => {
@@ -309,7 +311,7 @@ describe("CLI Update Command", () => {
 describe("CLI Add-Context Command", () => {
   beforeEach(async () => {
     // Ensure we have indexed files
-    await runQmd(["add", "."]);
+    await runQmd(["collection", "add", "."]);
   });
 
   test("adds context to a path", async () => {
@@ -332,7 +334,7 @@ describe("CLI Add-Context Command", () => {
 describe("CLI Cleanup Command", () => {
   beforeEach(async () => {
     // Ensure we have indexed files
-    await runQmd(["add", "."]);
+    await runQmd(["collection", "add", "."]);
   });
 
   test("cleans up orphaned entries", async () => {
@@ -352,7 +354,7 @@ describe("CLI Error Handling", () => {
   test("uses INDEX_PATH environment variable", async () => {
     // Verify the test DB path is being used by creating a separate index
     const customDbPath = join(testDir, "custom.sqlite");
-    const { exitCode } = await runQmd(["add", "."], {
+    const { exitCode } = await runQmd(["collection", "add", "."], {
       env: { INDEX_PATH: customDbPath },
     });
     expect(exitCode).toBe(0);
@@ -365,7 +367,7 @@ describe("CLI Error Handling", () => {
 
 describe("CLI Output Formats", () => {
   beforeEach(async () => {
-    await runQmd(["add", "."]);
+    await runQmd(["collection", "add", "."]);
   });
 
   test("search with --json flag outputs JSON", async () => {
@@ -399,8 +401,8 @@ describe("CLI Search with Collection Filter", () => {
     // Use a fresh database for this test suite
     localDbPath = getFreshDbPath();
     // Create multiple collections
-    await runQmd(["add", "notes/*.md"], { dbPath: localDbPath });
-    await runQmd(["add", "docs/*.md"], { dbPath: localDbPath });
+    await runQmd(["collection", "add", ".", "--mask", "notes/*.md"], { dbPath: localDbPath });
+    await runQmd(["collection", "add", ".", "--mask", "docs/*.md"], { dbPath: localDbPath });
   });
 
   test("filters search by collection name", async () => {
@@ -423,7 +425,7 @@ describe("CLI Context Management", () => {
     // Use a fresh database for this test suite
     localDbPath = getFreshDbPath();
     // Index some files first
-    await runQmd(["add", "."], { dbPath: localDbPath });
+    await runQmd(["collection", "add", "."], { dbPath: localDbPath });
   });
 
   test("add global context with /", async () => {
@@ -522,7 +524,7 @@ describe("CLI ls Command", () => {
     // Use a fresh database for this test suite
     localDbPath = getFreshDbPath();
     // Index some files first
-    await runQmd(["add", "."], { dbPath: localDbPath });
+    await runQmd(["collection", "add", "."], { dbPath: localDbPath });
   });
 
   test("lists all collections", async () => {
@@ -568,7 +570,7 @@ describe("CLI Collection Commands", () => {
     // Use a fresh database for this test suite
     localDbPath = getFreshDbPath();
     // Index some files first to create a collection
-    await runQmd(["add", "."], { dbPath: localDbPath });
+    await runQmd(["collection", "add", "."], { dbPath: localDbPath });
   });
 
   test("lists collections", async () => {

qmd.ts

@@ -2266,8 +2266,6 @@ function parseCLI() {
       files: { type: "boolean" },
       json: { type: "boolean" },
       collection: { type: "string", short: "c" },  // Filter by collection
-      // Add options
-      drop: { type: "boolean" },
       // Collection options
       name: { type: "string" },  // collection name
       mask: { type: "string" },  // glob pattern
@@ -2320,16 +2318,15 @@ function parseCLI() {
 
 function showHelp(): void {
   console.log("Usage:");
-  console.log("  qmd add [--drop] [glob]       - Add/update collection from $PWD (default: **/*.md)");
+  console.log("  qmd collection add [path] --name <name> --mask <pattern>  - Create/index collection");
+  console.log("  qmd collection list           - List all collections with details");
+  console.log("  qmd collection remove <name>  - Remove a collection by name");
+  console.log("  qmd ls [collection[/path]]    - List collections or files in a collection");
   console.log("  qmd context add [path] \"text\" - Add context for path (defaults to current dir)");
   console.log("  qmd context list              - List all contexts");
   console.log("  qmd context rm <path>         - Remove context");
   console.log("  qmd get <file>[:line] [-l N] [--from N]  - Get document (optionally from line, max N lines)");
   console.log("  qmd multi-get <pattern> [-l N] [--max-bytes N]  - Get multiple docs by glob or comma-separated list");
-  console.log("  qmd ls [collection[/path]]    - List collections or files in a collection");
-  console.log("  qmd collection list           - List all collections with details");
-  console.log("  qmd collection add [path] --name <name> --mask <pattern>  - Create collection explicitly");
-  console.log("  qmd collection remove <name>  - Remove a collection by name");
   console.log("  qmd status                    - Show index status and collections");
   console.log("  qmd update                    - Re-index all collections");
   console.log("  qmd embed [-f]                - Create vector embeddings (chunks ~6KB each)");
@@ -2379,17 +2376,6 @@ if (!cli.command || cli.values.help) {
 }
 
 switch (cli.command) {
-  case "add": {
-    const globArg = cli.args[0];
-    // Treat "." as "use default glob in current directory"
-    const globPattern = (!globArg || globArg === ".") ? DEFAULT_GLOB : globArg;
-    if (cli.values.drop) {
-      await dropCollection(globPattern);
-    }
-    await indexFiles(globPattern);
-    break;
-  }
-
   case "context": {
     const subcommand = cli.args[0];
     if (!subcommand) {