Refactor fit modes and sequential analysis workflow (#175)

* Rename Bayesian MAP labels to best posterior sample

* Add ADR for fit mode categories

* Refine fit-mode categories ADR with active-sibling pattern

* Add open questions and drop fitting.mode mirror in ADR

* Add implementation plan for fit-mode-categories ADR

* Rename CIF field _fitting.mode to _fitting.mode_type

* Tighten high-risk steps in fit-mode-categories plan

* Add BoolDescriptor for CIF-bound boolean values

* Add fitting category replacing fit configuration surface

* Add fitting_mode_type selector and fitting accessor on Analysis

* Rename joint_fit_experiments category to joint_fit

* Add sequential_fit category with persisted scan settings

* Add sequential_fit_extract category for scan metadata rules

* Replace fit category with Analysis.fit() method

* Drive sequential fitting from sequential_fit settings

* Auto-populate joint_fit rows and validate before fitting

* Add instance-aware help filter and hide inactive mode categories

* Serialize only active mode-specific analysis categories

* Restore mode before mode-specific analysis sections

* Update tutorials, docs, and exports for new fitting API

* Resolve ZIP extraction relative to saved project

* Add live progress tables for sequential fitting

* Set sequential fitting mode and save project

* Complete fit-mode categories and refactor progress

* Fix sequential replay, styling, and docs

* Simplify sequential progress table headers

* Add progress and time columns to sequential tables

* Unify sequential and single fit spinners on ActivityIndicator

* Fix spacing in chunk file range display

* Render sequential progress as bordered table with index column

* Render sequential progress with shared single-fit table renderable

* Add fit.series_all to plot every fitted parameter

* Unify fit.series to plot single or all fitted parameters

* Encapsulate chunk progress in dataclass

* Use string paths for versus parameter

* Unify ASCII plot width handling across terminal charts

* Sort ASCII parameter series by x before plotting

* Skip fit reports for sequential mode

* List all analysis files on save

* Bump dependencies

* Add resumed sequential-fit tutorial for Co2SiO4

* Update data index reference and hash

* Clear sequential fit state and make ZIP extraction explicit

* Update data index reference and hash

* Normalize sequential CSV paths for resumed fits

* Update data index reference and hash

* Add resume fit tutorial and fix paths

* Normalize CSV relative paths to POSIX style

* Remove project save step from tutorial

* Accept fit-mode categories ADR

* Move Quick Reference to end of nav

* Lower coverage threshold to 65%

Author: AndrewSazonov

docs/dev/ADR-suggestions/adr_parameter-posterior-summary.md

@@ -54,7 +54,7 @@ model.
 ### 2. Reuse the existing Bayesian summary container
 
 Do not add separate flat parameter attributes such as `median`,
-`map_estimate`, `interval_95`, `r_hat`, or `ess_bulk`.
+`best_sample_value`, `interval_95`, `r_hat`, or `ess_bulk`.
 
 Instead, the parameter-level projection reuses the existing
 `PosteriorParameterSummary` object already produced for
@@ -63,7 +63,7 @@ inspection, and later persistence.
 
 The summary object currently provides the right level of detail:
 
-- `map_estimate`
+- `best_sample_value`
 - `median`
 - `uncertainty`
 - `interval_68`
@@ -87,7 +87,7 @@ The internal field names stay compact and code-oriented. User-facing
 tables, summaries, and plot annotations should use these friendly
 labels:
 
-- `map_estimate` -> `MAP estimate`
+- `best_sample_value` -> `Best posterior sample`
 - `median` -> `Median`
 - `uncertainty` -> `Standard uncertainty`
 - `interval_68` -> `68% credible interval`
@@ -109,7 +109,7 @@ current_value = param.value
 current_uncertainty = param.uncertainty
 
 if param.posterior is not None:
-  map_estimate = param.posterior.map_estimate
+  best_sample_value = param.posterior.best_sample_value
   median = param.posterior.median
   uncertainty = param.posterior.uncertainty
   low95, high95 = param.posterior.interval_95
@@ -187,15 +187,15 @@ The exact helper names can be refined during implementation, but the
 design requirement is fixed: manual user edits clear stale metadata,
 while internal fit application installs fresh metadata atomically.
 
-### 8. Commit MAP to `parameter.value` after Bayesian fits
+### 8. Commit best posterior sample to `parameter.value` after Bayesian fits
 
 After a posterior-capable fit, `parameter.value` is committed from the
-maximum-a-posteriori estimate.
+best posterior sample.
 
-MAP is chosen because it is a coherent joint point estimate across all
-free parameters. Marginal medians remain available on
-`parameter.posterior`, but they are summary data rather than the active
-live model state.
+The best posterior sample is chosen because it is a coherent joint point
+estimate across all free parameters. Marginal medians remain available
+on `parameter.posterior`, but they are summary data rather than the
+active live model state.
 
 ### 9. Keep `uncertainty` as a convenience scalar after Bayesian fits
 
@@ -279,7 +279,7 @@ Stores one saved Bayesian result header with these fields:
 - `has_posterior_predictive`
 - `sidecar_file`
 
-For the current design, `point_estimate_name` is always `map`.
+For the current design, `point_estimate_name` is always `best_sample`.
 
 #### 11.3 `_bayesian_sampler` single item
 
@@ -320,7 +320,7 @@ Fields:
 - `order_index`
 - `unique_name`
 - `display_name`
-- `map_estimate`
+- `best_sample_value`
 - `median`
 - `uncertainty`
 - `interval_68_lower`
@@ -342,7 +342,7 @@ Fields:
 - `experiment_name`
 - `x_axis_name`
 - `x_path`
-- `map_prediction_path`
+- `best_sample_prediction_path`
 - `lower_95_path`
 - `upper_95_path`
 - `lower_68_path`
@@ -382,7 +382,7 @@ cosio.atom_site.Co2.adp_iso 0.0000 0.1200 4.0 0.0312 0.0021
 
 _bayesian_result.schema_version 1
 _bayesian_result.sampler_name dream
-_bayesian_result.point_estimate_name map
+_bayesian_result.point_estimate_name best_sample
 _bayesian_result.success yes
 _bayesian_result.sampler_completed yes
 _bayesian_result.reduced_chi_square 1.031
@@ -413,7 +413,7 @@ loop_
 _bayesian_parameter_posterior.order_index
 _bayesian_parameter_posterior.unique_name
 _bayesian_parameter_posterior.display_name
-_bayesian_parameter_posterior.map_estimate
+_bayesian_parameter_posterior.best_sample_value
 _bayesian_parameter_posterior.median
 _bayesian_parameter_posterior.uncertainty
 _bayesian_parameter_posterior.interval_68_lower
@@ -429,15 +429,15 @@ loop_
 _bayesian_predictive_dataset.experiment_name
 _bayesian_predictive_dataset.x_axis_name
 _bayesian_predictive_dataset.x_path
-_bayesian_predictive_dataset.map_prediction_path
+_bayesian_predictive_dataset.best_sample_prediction_path
 _bayesian_predictive_dataset.lower_95_path
 _bayesian_predictive_dataset.upper_95_path
 _bayesian_predictive_dataset.lower_68_path
 _bayesian_predictive_dataset.upper_68_path
 _bayesian_predictive_dataset.draws_path
 _bayesian_predictive_dataset.n_x
 _bayesian_predictive_dataset.n_draws_cached
-hrpt ttheta /predictive/hrpt/x /predictive/hrpt/map_prediction /predictive/hrpt/lower_95 /predictive/hrpt/upper_95 /predictive/hrpt/lower_68 /predictive/hrpt/upper_68 /predictive/hrpt/draws 2500 200
+hrpt ttheta /predictive/hrpt/x /predictive/hrpt/best_sample_prediction /predictive/hrpt/lower_95 /predictive/hrpt/upper_95 /predictive/hrpt/lower_68 /predictive/hrpt/upper_68 /predictive/hrpt/draws 2500 200
 ```
 
 ### 12. Persist bulk arrays in `analysis/bayesian_data.h5`
@@ -482,7 +482,7 @@ ordering.
 Recommended HDF5 dataset naming is:
 
 - `predictive__<experiment>__x`
-- `predictive__<experiment>__map_prediction`
+- `predictive__<experiment>__best_sample_prediction`
 - `predictive__<experiment>__lower_95`
 - `predictive__<experiment>__upper_95`
 - `predictive__<experiment>__lower_68`
@@ -497,7 +497,7 @@ Recommended HDF5 group layout is:
 - `/posterior/log_posterior`
 - `/posterior/draw_index`
 - `/predictive/<experiment>/x`
-- `/predictive/<experiment>/map_prediction`
+- `/predictive/<experiment>/best_sample_prediction`
 - `/predictive/<experiment>/lower_95`
 - `/predictive/<experiment>/upper_95`
 - `/predictive/<experiment>/lower_68`
@@ -573,7 +573,7 @@ param = project.phases['lbco'].cell.length_a
 posterior = param.posterior
 
 if posterior is not None:
-    print(posterior.map_estimate)
+  print(posterior.best_sample_value)
     print(posterior.uncertainty)
     print(posterior.interval_68)
 
@@ -673,7 +673,8 @@ It still defers:
 
 ## Chosen Defaults
 
-- `parameter.value` remains committed to MAP after posterior fits.
+- `parameter.value` remains committed to the best posterior sample after
+  posterior fits.
 - If a project is loaded without full posterior arrays, restoring only
   `parameter.posterior` is acceptable for table display and parameter
   inspection.

docs/dev/ADRs/adr_display-ux.md

@@ -77,7 +77,7 @@ project.display.parameters.cif_uids()
 
 project.display.fit.results()
 project.display.fit.correlations()
-project.display.fit.series(param, versus=temperature)
+project.display.fit.series(param, versus='diffrn.ambient_temperature')
 
 project.display.posterior.pairs()
 project.display.posterior.distribution(param)
@@ -197,7 +197,8 @@ Use these naming rules:
 - `fit.correlations()` shows parameter relationships from the latest
   fit.
 - `fit.series(param, versus=...)` shows fitted parameter values across a
-  sequence of fit results or experiments.
+  sequence of fit results or experiments, using a persisted `diffrn.*`
+  path for `versus`.
 - `posterior.*` names are used only when posterior samples are required.
 
 ## Rejected Alternatives
@@ -209,7 +210,7 @@ project.display.pattern(expt_name='hrpt')
 project.display.parameters(scope='free')
 project.display.fit_results()
 project.display.correlations()
-project.display.parameter_series(param, versus=temperature)
+project.display.parameter_series(param, versus='diffrn.ambient_temperature')
 project.display.posterior_pairs()
 project.display.posterior_distribution(param)
 project.display.posterior_predictive(expt_name='hrpt')