chore: initialize insar management system v2

experiments/isce2_sbas_timeseries/notes/PHASE2_BRIDGE_SMOKETEST_20260406.md

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+# Phase 2 Bridge Smoketest
+
+Date: 2026-04-06
+
+## Scope
+
+Validate the current SBAS bridge chain with the previously verified LT-1 sample stack:
+
+1. `build_lt1_stack_prep.py`
+2. `materialize_lt1_stack_scenes.py`
+3. `build_lt1_stack_prep.py` refresh
+
+This run validates the current bridge boundary only:
+
+- raw LT-1 scenes
+- local precise orbit pool
+- local prepared DEM
+- fresh scratch workspace
+
+It does not run:
+
+- `stripmapStack`
+- MintPy
+- geocode/export/publish
+
+## Inputs
+
+- sample manifest:
+  - `experiments/isce2_sbas_timeseries/configs/sample_stack_e123p3_n46p1.json`
+- orbit pool:
+  - `/mnt/d/orbit_pools/isce2`
+- DEM:
+  - `/mnt/z/Code/Insar_management_system_v2/experiments/isce2_sbas_timeseries/scratch/lt1a_strip1_hh_descending_e123p3_n46p1/inputs/dem/stack_dem_window.wgs84`
+
+## Workspace
+
+- scratch root:
+  - `experiments/isce2_sbas_timeseries/scratch/phase2_bridge_smoketest_20260406`
+
+## Result
+
+- final readiness: `True`
+- scene count: `5`
+- reference date: `20250510`
+- all orbits resolved: `True`
+- all `.slc/.slc.xml` present: `True`
+- all `data` shelves present: `True`
+
+## Materialization Summary
+
+- dates:
+  - `20250118`
+  - `20250315`
+  - `20250510`
+  - `20250705`
+  - `20250830`
+- status counts:
+  - `materialized: 5`
+- total bytes written:
+  - `16313641344`
+
+## Artifacts
+
+- selected manifest used for this WSL run:
+  - `experiments/isce2_sbas_timeseries/scratch/phase2_bridge_smoketest_20260406/selected_stack_manifest_wsl.json`
+- generated stack manifest:
+  - `experiments/isce2_sbas_timeseries/scratch/phase2_bridge_smoketest_20260406/stack_input_manifest.json`
+- materialization summary:
+  - `experiments/isce2_sbas_timeseries/scratch/phase2_bridge_smoketest_20260406/materialization_summary.json`
+- generated stack dry-run wrapper:
+  - `experiments/isce2_sbas_timeseries/scratch/phase2_bridge_smoketest_20260406/run_stripmap_stack_dryrun.sh`
+- synthetic water-mask recovery report:
+  - `experiments/isce2_sbas_timeseries/scratch/phase2_bridge_smoketest_20260406/stack_work/logs/run_01_reference.synthetic_watermask.json`
+
+## Finding
+
+`build_lt1_stack_prep.py` currently reads `scene["tiff_path"]` and `scene["meta_path"]` directly.
+When the script is run inside WSL against the sample manifest, the original `F:\...` Windows paths are not readable as Linux paths.
+
+For this smoketest, a temporary WSL-path manifest copy was generated and used:
+
+- `selected_stack_manifest_wsl.json`
+
+This is an experiment-side workaround only.
+No production/system logic was changed for this run.
+
+## Update 2026-04-07
+
+The same fresh workspace was then continued through the stripmap stack run files.
+
+### Additional Result
+
+- `run_01_reference`
+  - reached `createWaterMask`
+  - failed on remote `SWBD` retrieval from:
+    - `https://e4ftl01.cr.usgs.gov/MEASURES/SRTMSWBD.003/...`
+  - recovered with a local synthetic all-land `waterMask.rdr`
+- `run_02_focus_split`
+  - completed
+- `run_03_geo2rdr_coarseResamp`
+  - completed
+- `run_04_refineSecondaryTiming`
+  - completed
+- `run_05_invertMisreg`
+  - completed
+- `run_06_fineResamp`
+  - completed
+- `run_07_grid_baseline`
+  - completed
+- `run_08_igram`
+  - completed through interferogram generation, filtering, coherence, and `snaphu` unwrapping
+
+### Interferogram Snapshot
+
+- pair count on disk:
+  - `10`
+- verified pair folders:
+  - `20250118_20250315`
+  - `20250118_20250510`
+  - `20250118_20250705`
+  - `20250118_20250830`
+  - `20250315_20250510`
+  - `20250315_20250705`
+  - `20250315_20250830`
+  - `20250510_20250705`
+  - `20250510_20250830`
+  - `20250705_20250830`
+- verified key files in every pair directory:
+  - `filt_<date12>.int`
+  - `filt_<date12>.cor`
+  - `filt_<date12>_snaphu.unw`
+  - `filt_<date12>_snaphu.unw.conncomp`
+
+### Finding Update
+
+The original `run_generated_stack_runfile_ubuntu2404.sh` fallback only matched the `.netrc` credential failure text.
+This workspace showed a second offline failure mode:
+
+- `createWaterMask` started normally
+- ISCE2 `DataRetriever` failed during `SWBD` file retrieval
+- the wrapper therefore did not auto-recover on the first attempt
+
+The experiment helper has now been widened to recognize both:
+
+- missing Earthdata credential text
+- direct `SWBD` retrieval failure text from `createWaterMask`
+
+No production/system runtime was changed by this fix.
+
+## Recommended Next Step
+
+Use this fresh workspace to continue with:
+
+1. unified-env MintPy smoketest using:
+   - `configs/phase2_bridge_smoketest_20260406_smallbaseline.cfg`
+2. publish-style geocode/export if MintPy succeeds
+3. compare this fresh replay with the earlier baseline workspace