chore(commands): remove deprecated validate command, update count to 63 (closes #100)

[Wolfvin]

Summary

Closes #100.

The validate command was deprecated several versions ago with a "renamed to registry-validate" message. This PR removes the deprecated alias entirely, dropping the CLI command count from 64 → 63.

Changes

Removed

• scripts/commands/validate.py — the deprecated alias module (its register_command("validate", ...) call was the only thing keeping the command registered). Commands are auto-imported from scripts/commands/, so deleting the file is sufficient to unregister the command.
• _TOOL_DEFINITIONS["validate"] entry in scripts/mcp_server.py — the static MCP tool schema for codelens_validate. Without this removal, the MCP server would still advertise codelens_validate even though the underlying command no longer exists (callers would get "Unknown command: validate"). codelens_registry_validate continues to work as a dynamic tool, unchanged.
• _md_validate() function and its dispatch entry in scripts/formatters/markdown.py — dead code path for the removed command. registry-validate continues to use the generic markdown formatter (no behavior change).

Updated

• scripts/codelens.py:
  • Top-level docstring usage example: validate → registry-validate.
  • _REGISTRY_COMMANDS set: removed "validate" (it was a dead entry; the auto-setup block only runs when args.command is in COMMAND_REGISTRY, which validate no longer is).
• scripts/commands/registry_validate.py: docstring updated to note the deprecated alias was removed in [CHORE] Remove deprecated validate command — already replaced by registry-validate #100 (previously pointed at validate.py). Help text simplified — no more "(renamed from validate)" suffix.
• tests/test_integration.py:
  • NO_ARGS_COMMANDS list: removed "validate" (was parametrizing a smoke test against a command that no longer exists).
  • EXPECTED_COMMAND_COUNT sentinel: 64 → 63 (this is the one place the count is allowed to be hardcoded, per the file's own docstring — sync_command_count.py intentionally does not touch it).
• README.md command table: validate [workspace] → registry-validate [workspace].
• SKILL-QUICK.md Setup & Lifecycle section: validate → registry-validate.

Synced via python3 scripts/sync_command_count.py --apply

The single-source-of-truth sync script auto-updated the command/MCP counts in:

• README.md (5 substitutions: 64 → 63, 62 → 61, 51 → 50 in multiple places)
• SKILL.md (2 substitutions: 64 → 63, 62 → 61)
• SKILL-QUICK.md (5 substitutions: 64 → 63, 62 → 61, plus the Total: N commands line)
• pyproject.toml (1 substitution: 64 → 63)
• skill.json (1 substitution: 64 → 63)
• scripts/graph_model.py (1 substitution: 64 → 63 in docstring)
• tests/test_integration.py module docstring (1 substitution: 64 → 63)

Manual count fixes (sync script regex did not match — pre-existing gaps)

• scripts/mcp_server.py line 7: 64 → 63 in module docstring (sync regex requires \d+\+ but file has plain \d+).
• SKILL-QUICK.md line 160: 51 → 50 statically-defined tools (sync regex requires including ... suffix that no longer exists in the file).

Verification — Definition of Done

#	Check	Result
1	codelens validate returns "unrecognized command"	✅ error: argument command: invalid choice: 'validate'
2	codelens registry-validate still works normally	✅ Returns valid JSON, status ok
3	PYTHONUTF8=1 python scripts/codelens.py --command-count returns 63	✅ 63
4	PYTHONUTF8=1 python -m pytest tests/ --ignore=tests/test_integration.py — no regression	✅ Baseline: 788 passed, 87 skipped → Post-fix: 788 passed, 87 skipped

Additional checks:

• python3 scripts/sync_command_count.py --check reports All documentation files are in sync with COMMAND_REGISTRY.
• tests/test_command_count.py — all 4 doc-sync tests pass.

Constraints honored

• registry-validate is not affected in any functional way. It is still registered, still callable from the CLI, still exposed as the codelens_registry_validate MCP tool with the same dynamic schema as before.
• No test that exercised the deprecated validate deprecation message was found in the non-integration suite — the only test that mentioned validate as a command was tests/test_integration.py (ignored by DoD), and its NO_ARGS_COMMANDS list was updated.

Findings (out of scope, not fixed)

• scripts/sync_command_count.py has two stale regex rules that no longer match the current file contents:
  1. The mcp_server.py rule requires \d+\+ but the file uses plain \d+ (so the count must be updated manually whenever it changes).
  2. The SKILL-QUICK.md "statically-defined tools" rule requires an including ... suffix that was removed in a previous edit.
     Both are pre-existing — they caused the sync script to silently skip these files. Worth a follow-up issue to tighten the regexes.

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[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

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