Fix duplicate flag definition and task resolution logic (#28)

* Initial plan

* Fix duplicate flag and task file finding logic

Co-authored-by: alexec <1142830+alexec@users.noreply.github.com>

* Update README with new flags and memory file formats

Co-authored-by: alexec <1142830+alexec@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: alexec <1142830+alexec@users.noreply.github.com>

Author: Copilot

README.md

@@ -82,19 +82,42 @@ coding-context [options] <task-name>
 
 Options:
   -b                Automatically run the bootstrap script after generating it
-  -d <directory>    Add a directory to include in the context (can be used multiple times)
+  -d <directory>    Directory that may contain a memories/ or tasks/ subdirectory (can be used multiple times)
                     Default: .prompts, ~/.config/prompts, /var/local/prompts
+  -m <path>         Directory containing memories, or a single memory file (can be used multiple times)
+                    Default: AGENTS.md
+  -t <path>         Directory containing tasks, or a single task file (can be used multiple times)
   -o <directory>    Output directory for generated files (default: .)
   -p <key=value>    Template parameter for prompt substitution (can be used multiple times)
   -s <key=value>    Include memories with matching frontmatter (can be used multiple times)
   -S <key=value>    Exclude memories with matching frontmatter (can be used multiple times)
 ```
 
+**Important:** The task file name **MUST** match the task name you provide on the command line. For example, if you run `coding-context my-task`, the tool will look for `my-task.md` in the task directories.
+
 **Example:**
 ```bash
 coding-context -p feature="Authentication" -p language=Go add-feature
 ```
 
+**Example with directories:**
+```bash
+# Add a custom directory that contains memories/ and tasks/ subdirectories
+coding-context -d /path/to/custom/prompts my-task
+
+# The -d flag prepends directories to search paths, so custom directories take priority
+# Search order becomes: /path/to/custom/prompts/memories, .prompts/memories, ~/.config/prompts/memories, ...
+```
+
+**Example with custom memory and task paths:**
+```bash
+# Specify explicit memory files or directories
+coding-context -m .github/copilot-instructions.md -m CLAUDE.md my-task
+
+# Specify custom task directory
+coding-context -t ./custom-tasks my-task
+```
+
 **Example with selectors:**
 ```bash
 # Include only production memories
@@ -131,6 +154,8 @@ Memory files are included in every generated context. They contain reusable info
 
 Prompt files define specific tasks. They can use template variables (like `${taskName}` or `$taskName`) that you provide via command-line parameters.
 
+**IMPORTANT:** The file name **MUST** match the task name you'll use on the command line. For example, a file named `my-task.md` is invoked with `coding-context my-task`.
+
 ```markdown
 # Task: ${taskName}
 
@@ -183,6 +208,10 @@ Each directory should contain:
 
 Markdown files with YAML frontmatter and Go template support.
 
+**CRITICAL:** The prompt file name (without the `.md` extension) **MUST** exactly match the task name you provide on the command line. For example:
+- To run `coding-context add-feature`, you need a file named `add-feature.md`
+- To run `coding-context my-custom-task`, you need a file named `my-custom-task.md`
+
 **Example** (`.prompts/tasks/add-feature.md`):
 ```markdown
 # Task: ${feature}
@@ -195,6 +224,8 @@ Run with:
 coding-context -p feature="User Login" -p language=Go add-feature
 ```
 
+This will look for `add-feature.md` in the task directories.
+
 ### Memory Files
 
 Markdown files included in every generated context. Bootstrap scripts can be provided in separate files.
@@ -218,6 +249,36 @@ npm install
 
 For each memory file `<name>.md`, you can optionally create a corresponding `<name>-bootstrap` file that will be executed during setup.
 
+### Supported Memory File Formats
+
+This tool can work with various memory file formats used by popular AI coding assistants. By default, it looks for `AGENTS.md` in the current directory. You can also specify additional memory files or directories using the `-m` flag.
+
+#### Common Memory File Names
+
+The following memory file formats are commonly used by AI coding assistants and can be used with this tool:
+
+- **`AGENTS.md`** - Default memory file (automatically included)
+- **`.github/copilot-instructions.md`** - GitHub Copilot instructions file
+- **`CLAUDE.md`** - Claude-specific instructions
+- **`.cursorrules`** - Cursor editor rules (if in Markdown format)
+- **`.cursor/rules/`** - Directory containing Cursor-specific rule files
+- **`.instructions.md`** - General instructions file
+- **`.continuerules`** - Continue.dev rules (if in Markdown format)
+
+**Example:** Using multiple memory sources
+```bash
+# Include GitHub Copilot instructions and CLAUDE.md
+coding-context -m .github/copilot-instructions.md -m CLAUDE.md my-task
+
+# Include all rules from Cursor directory
+coding-context -m .cursor/rules/ my-task
+
+# Combine default AGENTS.md with additional memories
+coding-context -m .instructions.md my-task
+```
+
+**Note:** All memory files should be in Markdown format (`.md` extension) or contain Markdown-compatible content. The tool will automatically process frontmatter in YAML format if present.
+
 
 ## Filtering Memories with Selectors
 

main.go

@@ -48,7 +48,6 @@ func main() {
 		"AGENTS.md",
 	}
 
-	flag.Var(&dirs, "d", "Directory to include in the context. Can be specified multiple times.")
 	flag.Var(&dirs, "d", "Directory that may contain a memories/ or tasks/ subdirectory. Can be specified multiple times.")
 	flag.Var(&memories, "m", "Directory containing memories, or a single memory file. Can be specified multiple times.")
 	flag.Var(&tasks, "t", "Directory containing tasks, or a single task file. Can be specified multiple times.")
@@ -184,7 +183,7 @@ func run(ctx context.Context, args []string) error {
 			continue
 		}
 		if stat.IsDir() {
-			path = filepath.Join(path, stat.Name())
+			path = filepath.Join(path, taskName+".md")
 			if _, err := os.Stat(path); os.IsNotExist(err) {
 				continue
 			}