indexer: handle missing parent objects in shallow clones and root commits

[Vui-Chee]

Problem

Running semcode-index --source /path/to/repo without --git fails with:

Error: An object with id 69695f5331d4d670eff76376faa3aeb5d68733e3 could not be found

This happens on:

• Shallow clones (git clone --depth 1) — the HEAD commit has parent SHAs recorded in it, but those parent objects are not present in the local object store
• Root commits — repos initialized from tarballs (e.g. git init && git add . && git commit) with no parent at all

Root Cause

When no --git flag is provided, run_pipeline auto-detects HEAD and constructs the range SHA^..SHA (parent-to-HEAD). list_shas_in_range then calls resolve_to_commit(repo, "SHA^"), which gix implements by looking up the parent object in the local store — failing with the above error when it doesn't exist.

Fix

In list_shas_in_range, catch the error from resolving from_spec and fall back to returning just [to_commit_sha]. This means indexing proceeds with the single HEAD commit, which is the correct behaviour for the auto-detect case.

Test

# Shallow clone
git clone --depth 1 https://github.com/torvalds/linux linux-shallow
semcode-index --source linux-shallow --database ./linux-shallow.db

# Tarball-initialized repo
tar xf linux-6.18.6.tar.xz && cd linux-6.18.6
git init && git add . && git commit -m "initial"
semcode-index --source . --database ./code.db

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