docs: fix two documentation drift issues in tools/skill_generator/README.md

[bipinhcs11]

What and why

Two documentation drift issues in tools/skill_generator/README.md that have been present since the feat/skill-validator (PR #5) and feat/skill-gen-doctor (PR #8) merges.

1. validate and doctor missing from the Subcommand map table

The subcommand map listed 9 subcommands but the CLI (cli.py) exposes 11. validate and doctor were added in earlier PRs but never reflected in the README's own index. Any developer who reads the table to discover what commands are available won't find two of them.

2. bin/ incorrectly listed as a silently skipped directory

The "What Stage 1 skips" paragraph claimed bin/ is silently skipped. The code disagrees:

DEFAULT_EXCLUDE_DIRS = {
    "target", "build", ".git", "generated", ".mvn",
    "node_modules", ".idea", ".vscode", ".gradle",
    "out", "dist", ".settings",
    # Note: "bin/" intentionally NOT excluded — legacy apps put shell scripts there.
    # Eclipse compiled output (.class files) inside bin/ is still filtered by BINARY_EXTENSIONS.
}

bin/ is intentionally absent. A developer reading the README to understand what the crawler walks would assume bin/ is safe to fill with output — the opposite of the intended behaviour.

Changes

Location	Change
Subcommand map table	Add validate and doctor rows
"What Stage 1 skips"	Remove bin/ from the excluded-dirs list; add a note explaining it is intentionally NOT excluded and why

No logic changes

Pure documentation fix. All 172 tests pass unchanged.

Follow-ups (not in this PR)

• Open PRs test: smoke tests for update.py — last uncovered module #12 / test: smoke tests for update.py (Phase 2 incremental updater) #14 / test: smoke tests for update.py (was the only uncovered module) #17 / test: smoke tests for update.py pure functions (Phase 2 updater) #19 all add tests/test_update.py; one of them should be merged and the rest closed.
• PR chore: bump TOOL_VERSION to 0.3.0 and fix stale module README #13 bumps TOOL_VERSION and also edits this README (the version string and schema example at the bottom). If that merges first, a trivial rebase of this PR is needed.

https://claude.ai/code/session_01JiDRe3frmV8eeK53c8GHnp

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