Grafema URI Semantic ID Parsing

Problem

Code that processes semantic IDs using split("->") silently fails when the analysis pipeline has converted IDs to grafema:// URI format. The URI format uses # fragments with percent-encoded characters (%3E instead of >), so -> never appears and split("->") returns the entire string as element 0.

Context / Trigger Conditions

• Derived edges (e.g., MODULE->MODULE DEPENDS_ON from IMPORTS_FROM) produce 0 results
• File path extraction from semantic IDs returns the whole URI string
• Any Rust code in the orchestrator that processes semantic IDs from RFDB after to_uri_format() has been called during analysis
• Lookups into file_to_module or similar file-keyed maps always miss

The Two Formats

Legacy compact format (before to_uri_format):

src/components/App.tsx->IMPORT_BINDING->react
MODULE#src/components/App.tsx

URI format (after to_uri_format, stored in RFDB):

grafema://github.com/owner/repo/src/components/App.tsx#IMPORT_BINDING%3Ereact
grafema://github.com/owner/repo/src/components/App.tsx#MODULE

Virtual nodes (no file path):

grafema://github.com/owner/repo/_/EXTERNAL_MODULE%3Elodash
grafema://github.com/owner/repo/_/GLOBAL%3A%3Aconsole

Solution

Always handle both formats when extracting file paths from semantic IDs:

// Pre-compute URI prefix (authority is known from resolve_authority())
let uri_prefix = format!("grafema://{authority}/");

let extract_file = |id: &str| -> &str {
    if let Some(rest) = id.strip_prefix(&uri_prefix) {
        // URI format: take path up to '#'
        rest.split('#').next().unwrap_or("")
    } else {
        // Legacy format: take path up to first '->'
        id.split("->").next().unwrap_or("")
    }
};

Key points:

• authority is always available via resolve_authority(&cfg) in main.rs
• Virtual nodes have _/ as the file path component — these won't match real files (correct behavior)
• node.file fields stay as relative paths (not URI-formatted), so file_to_module maps use relative paths as keys
• Edge src/dst fields ARE URI-formatted (they reference node IDs which were converted)

Verification

After fixing, check:

1. all_imports_from_edges.len() > 0 (edges are collected)
2. depends_on_pairs.len() > 0 (file paths extracted and matched)
3. Tracing output shows "Module dependency edges derived" with non-zero count

Example: The DEPENDS_ON Bug

The to_uri_format() method in analyzer.rs converts node IDs but keeps node.file as-is:

pub fn to_uri_format(&mut self, authority: &str) {
    for node in &mut self.nodes {
        node.id = convert(&node.id);  // → grafema://authority/path#FRAGMENT
        // node.file stays as relative path
    }
    for edge in &mut self.edges {
        edge.src = convert(&edge.src);  // → URI format
        edge.dst = convert(&edge.dst);  // → URI format
    }
}

So IMPORTS_FROM edges in RFDB have URI-formatted src/dst, but MODULE nodes have relative file paths. The derivation code must parse URIs to extract relative paths for the file_to_module lookup.

Notes

• This affects ALL code that processes semantic IDs from RFDB in the orchestrator
• The compact_to_uri function in analyzer.rs defines the exact URI structure
• Fragment encoding: > → %3E, [ → %5B, ] → %5D, # → %23
• If authority changes between runs, old and new URIs won't match