fix(cli): refuse an implicit home root and cap omissions

[EnRaiha]

Why

An agent session runs with the working directory set to the user's home, so selecting the current directory as the project walked ~2.4M files, ran past any subprocess timeout, and produced no output at all.

A wide root also omits one entry per skipped file: a status envelope for /tmp carried 22,933 entries and 9 MB of JSON, and both the project and cached lists duplicated it.

What

• Refuse an implicit root that is a home directory or the filesystem root, naming the fix in the error. An explicit --root still selects whatever the caller asks for.
• Cap each reported omission list at 256 entries, keep the full count in omittedFiles / omitted_files (new on IndexOutput), and mark a capped list with omissionsTruncated.
• Human output names the truncation and reports the index total from the count instead of the list length.

Tests

• implicit_cwd_root_refuses_home_and_filesystem_root_only (cli/src/project/select.rs)
• omission_entry_lists_are_capped_while_the_truncation_is_reported (cli/src/result.rs)
• cargo test -p code2graph-cli — 20 pass

[Copilot]

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[farhan-syah]

The accidental home scan and oversized omission envelopes deserve this focused change. The Windows home guard needs correction before merging. Preserve complete reason totals when truncating diagnostic entries.

Checks pass on Linux:

• cargo test -p code2graph-cli --offline: 253 unit tests and 20 integration tests.
• cargo fmt --all -- --check.
• cargo clippy -p code2graph-cli --all-targets --offline -- -D warnings.

The Windows finding follows the documented canonical path representation. I did not run Windows tests locally.

[farhan-syah]

Both review findings are resolved.

Finding	Resolution
Canonical home comparison	Home and cwd now use canonical paths. Explicit selection bypasses home discovery.
Full omission reason counts	Index and status retain complete reason totals while diagnostic entries remain capped at 256.

Regression coverage checks actual selection paths, Windows prefixes, and mixed reasons outside the entry cap.

Checks:

• All nine CI jobs pass, including Linux, macOS, and Windows tests.
• Local CLI tests pass: 255 unit tests and 20 integration tests.
• Formatting, CLI lint, and documentation checks pass.