fix: accept 4+ digit spec numbers in tests and docs (#2094)

Two test assertions in test_timestamp_branches.py used the regex
`\d{3}` (exactly 3 digits) instead of `\d{3,}` (3 or more digits).
While the underlying shell scripts already handle spec numbers ≥ 1000
correctly — printf "%03d" and PowerShell '{0:000}' both expand naturally
beyond 3 digits, and all detection regexes use {3,} — the overly-strict
test assertions would fail with a misleading error if a fixture ever
contained 1000+ spec directories.

Documentation in README.md, spec-driven.md, and the CLI --branch-numbering
help text implied that sequential spec numbers are always 3 digits, which
could lead users to believe a hard limit of 999 exists.

Changes:
- tests/test_timestamp_branches.py: change two \d{3} assertions to \d{3,}
- src/specify_cli/__init__.py: clarify help text to show numbers expand past 999
- README.md: update --branch-numbering docs to note numbers expand beyond 3 digits
- spec-driven.md: update feature numbering description to include 4-digit example

Fixes #2093

Co-authored-by: alex-zwingli <alex-zwingli@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: alex-zwingli

README.md

@@ -337,7 +337,7 @@ The `specify` command supports the following options:
 | `--debug`              | Flag     | Enable detailed debug output for troubleshooting                                                                                                                                                                                                                                                                                                                                          |
 | `--github-token`       | Option   | GitHub token for API requests (or set GH_TOKEN/GITHUB_TOKEN env variable)                                                                                                                                                                                                                                                                                                                 |
 | `--ai-skills`          | Flag     | Install Prompt.MD templates as agent skills in agent-specific `skills/` directory (requires `--ai`). Extension commands are also auto-registered as skills when extensions are added later.                                                                                                                                                                                               |
-| `--branch-numbering`   | Option   | Branch numbering strategy: `sequential` (default — `001`, `002`, `003`) or `timestamp` (`YYYYMMDD-HHMMSS`). Timestamp mode is useful for distributed teams to avoid numbering conflicts                                                                                                                                                                                                  |
+| `--branch-numbering`   | Option   | Branch numbering strategy: `sequential` (default — `001`, `002`, `003`, …, `1000`, … — expands beyond 3 digits automatically) or `timestamp` (`YYYYMMDD-HHMMSS`). Timestamp mode is useful for distributed teams to avoid numbering conflicts                                                                                                                                                                                                  |
 
 ### Examples
 

spec-driven.md

@@ -78,7 +78,7 @@ The SDD methodology is significantly enhanced through three powerful commands th
 
 This command transforms a simple feature description (the user-prompt) into a complete, structured specification with automatic repository management:
 
-1. **Automatic Feature Numbering**: Scans existing specs to determine the next feature number (e.g., 001, 002, 003)
+1. **Automatic Feature Numbering**: Scans existing specs to determine the next feature number (e.g., 001, 002, 003, …, 1000 — expands beyond 3 digits automatically)
 2. **Branch Creation**: Generates a semantic branch name from your description and creates it automatically
 3. **Template-Based Generation**: Copies and customizes the feature specification template with your requirements
 4. **Directory Structure**: Creates the proper `specs/[branch-name]/` structure for all related documents

src/specify_cli/__init__.py

@@ -840,7 +840,7 @@ def init(
     ai_skills: bool = typer.Option(False, "--ai-skills", help="Install Prompt.MD templates as agent skills (requires --ai)"),
     offline: bool = typer.Option(False, "--offline", help="Deprecated (no-op). All scaffolding now uses bundled assets.", hidden=True),
     preset: str = typer.Option(None, "--preset", help="Install a preset during initialization (by preset ID)"),
-    branch_numbering: str = typer.Option(None, "--branch-numbering", help="Branch numbering strategy: 'sequential' (001, 002, ...) or 'timestamp' (YYYYMMDD-HHMMSS)"),
+    branch_numbering: str = typer.Option(None, "--branch-numbering", help="Branch numbering strategy: 'sequential' (001, 002, …, 1000, … — expands past 999 automatically) or 'timestamp' (YYYYMMDD-HHMMSS)"),
     integration: str = typer.Option(None, "--integration", help="Use the new integration system (e.g. --integration copilot). Mutually exclusive with --ai."),
     integration_options: str = typer.Option(None, "--integration-options", help='Options for the integration (e.g. --integration-options="--commands-dir .myagent/cmds")'),
 ):

tests/test_timestamp_branches.py

@@ -134,7 +134,7 @@ def test_sequential_default_with_existing_specs(self, git_repo: Path):
             if line.startswith("BRANCH_NAME:"):
                 branch = line.split(":", 1)[1].strip()
         assert branch is not None
-        assert re.match(r"^\d{3}-new-feat$", branch), f"unexpected branch: {branch}"
+        assert re.match(r"^\d{3,}-new-feat$", branch), f"unexpected branch: {branch}"
 
     def test_sequential_ignores_timestamp_dirs(self, git_repo: Path):
         """Sequential numbering skips timestamp dirs when computing next number."""
@@ -289,7 +289,7 @@ def test_e2e_sequential(self, git_repo: Path):
             capture_output=True,
             text=True,
         ).stdout.strip()
-        assert re.match(r"^\d{3}-seq-feat$", branch), f"branch: {branch}"
+        assert re.match(r"^\d{3,}-seq-feat$", branch), f"branch: {branch}"
         assert (git_repo / "specs" / branch).is_dir()
         val = source_and_call(f'check_feature_branch "{branch}" "true"')
         assert val.returncode == 0