codegraph_index_markdown` overwrites previously indexed documents in v0.19.1

[finix7776]

Environment

• CodeGraph: 0.19.1
• Build: ef6a466
• Platform: macOS ARM64
• Transport: MCP through a resident --serve engine and --connect client
• Client: OpenAI Codex

Description

Indexing multiple Markdown files does not preserve all previously indexed
documents.

codegraph_index_markdown returns status: success, but after indexing another
file, previously indexed sources or chunks disappear from
codegraph_list_doc_sources and can no longer be found with
codegraph_search_docs.

The issue still occurs with only one resident CodeGraph engine and one connected
client. All VS Code CodeGraph processes were disabled before reproducing it.

Minimal reproduction

Create two files:

a.md

# Alpha

unique-alpha-marker

b.md

# Beta

unique-beta-marker

Then run:

1. codegraph_index_markdown(path: "/tmp/a.md")
2. codegraph_list_doc_sources()
3. codegraph_index_markdown(path: "/tmp/b.md")
4. codegraph_list_doc_sources()
5. Search for both unique markers with codegraph_search_docs.

Actual behavior

After indexing the second file, sections belonging to the first file can
disappear.

The response also appears to generate chunk IDs starting again from
doc-0001 for every source. This may cause collisions between chunks from
different Markdown files.

Expected behavior

Indexing a new Markdown source should add its chunks without removing chunks
belonging to other sources.

Chunk identifiers should be unique across sources, for example by including a
source-path hash or another stable namespace.

Additional evidence

The server documentation says that re-indexing should replace data only for the
same source file. In this case, indexing a different source affects previously
indexed sources.